- add(hapIds) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdMultiset
-
Method to increment the count for a given hapId set
- add(kmer) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerCounter
-
Add kmer by Long representation as defined by BaseEncoder (fast)
- add(kmerAsByte) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerCounter
-
Add kmer by byte array
- add(kmer) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerCounter
-
Add kmers by String representation of DNA - slowest way if lots of overlapping kmers
- add(kmer, occurrences) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerCounter
-
- add(kmer, occurrences) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerCounter
-
- addAll(newKmerCounts) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerCounter
-
- addAll(sequence) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerCounter
-
Add kmer sequence using the previously defined kmerSize, stepSize, and kmerPrefix (very fast)
- addAll(otherMap) - Method in class net.maizegenetics.pangenome.hapCalling.PositionToRefAndAltHaplotypes
-
- addBestReadMapToHapIdMultiset(bestReadMap, hapIdToRefRangeMap, maxRefRangeError, pairedEnd, hapIdMultiset, hapIdToStatMap) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
- addDNASeqToMap(dna) - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- addHeadersToOutputFiles(writers, fileGroupName, methodName, methodDescription) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
- addIdentityToMap(wiggleFile, chromMap) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function to load in the identity/coverage into the full map.
- addInGQBlockHeader(headerLines) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
- addInIndels(range, refSequence, consensusSequences, rawConsensusWithIndels, minComparableIndels, mergeRule) - Static method in class net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus
-
Method to add in the indels which were removed for the merging process. The indels need to be readded in due to the filtering process in MergeGVCFPlugin. There we removed all sites where there was an indel in any of the taxa. Even if it was just one. Because of this, we likely have a lot of reference alleles missing from the consensus for the majority of the taxa. This method will add in any calls which are in agreement by all the taxon in the cluster or in the case of disagreement it will use the INDEL_MERGE_RULE to determine what variantContext record to put back in.
- addMissingSequenceNodes(graph) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
- addMissingSequenceNodes(result) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
- addPathsToGraph(inGraph) - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
- AddPathsToGraphPlugin - Class in net.maizegenetics.pangenome.api
-
This class is used to add path information to an existing graph to provide more information
for calculating transition probabilities for finding new paths. If the paths contain haplotypes not included in the
original graph they will be added without variant info or seuences. The reason is that the plugin results will be used by
path finding, which does not use either variant info or sequence.
- AddPathsToGraphPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
This class is used to add path information to an existing graph to provide more information
for calculating transition probabilities for finding new paths. If the paths contain haplotypes not included in the
original graph they will be added without variant info or seuences. The reason is that the plugin results will be used by
path finding, which does not use either variant info or sequence.
- AddPathsToGraphPlugin() - Constructor for class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
This class is used to add path information to an existing graph to provide more information
for calculating transition probabilities for finding new paths. If the paths contain haplotypes not included in the
original graph they will be added without variant info or seuences. The reason is that the plugin results will be used by
path finding, which does not use either variant info or sequence.
- AddPathsToGraphPluginKt - Class in net.maizegenetics.pangenome.api
-
- addRange(geneRange, range, gene) - Static method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- addRange(geneRange, range, currentLine, overlappingPosition) - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
- addRange(originalRangeMap, newRange, newCall) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
addRange method adapted from Louis Wasserman's(author of RangeMap) answer here: https://stackoverflow.com/questions/41418416/intersecting-ranges-when-using-rangemap This method will concatenate the string if the range overlaps an existing range in the map. Because VCF files should be ordered(in the spec) the concatenation should be ordered correctly
- addRange(originalRangeMap, newRange, newCall) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
addRange method adapted from Louis Wasserman's(author of RangeMap) answer here: https://stackoverflow.com/questions/41418416/intersecting-ranges-when-using-rangemap This method will concatenate the string if the range overlaps an existing range in the map. Because VCF files should be ordered(in the spec) the concatenation should be ordered correctly
- AddRefRangeAsAssemblyPlugin - Class in net.maizegenetics.pangenome.db_loading
-
This function is fairly obsolete. IT was used before the graph was able to take multiple methods as parameters. This class created to load a reference genome as an assembly. The method is hard-coded to "mummer4", which is the assembly method name at the time of this writing. All the variants are reference records. The addition of these haplotypes allows for pulling TODO: IT it is deemd this class is still useful, it should be updated to create a gvcf file as is done in LoadAllIntervalsToPHGdbPlugin, store the gvcf file data to the genomeFileData table, and save the gvcfFileId to the anchorDataPHG object.
- AddRefRangeAsAssemblyPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
- AddRefRangeAsAssemblyPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
- AddRefRangeAsAssemblyPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
- AddRefRangeGroupPlugin - Class in net.maizegenetics.pangenome.db_loading
-
This class creates a user defined ref range group, adds it to the specified db, associates requested reference ranges with the new group. Input: 1. anchor bed file: Should be a subset of reference ranges currently existing in the DB. Format is tab-delimited file with columns: chr startpos endpos No header, positions are BED file formatted, ie 0-based, inclusive/exclusive 2. Name for the new method, which is the ref range group. 3. Method details: user description for method 4. Config file with db connection info Output: 1. Database tables "methods" and "ref_range_ref_range_method" are updated. Algorithm: 1. Read bed file into an object 2. Read all reference ranges from db 3. Verify all entries from the bed file exist in the reference_ranges table (throw exception if false) 4. Verify method name does not exist in methods table (throw exception if false) 5. Add method name to db. 6. Add specified reference ranges to the ref_range_ref_range_methods table with method_id = new method id.
- AddRefRangeGroupPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
- AddRefRangeGroupPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
- AddRefRangeGroupPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
- addSequenceDictionary(vcfheader, refGenomeSequence) - Static method in class net.maizegenetics.pangenome.db_loading.VariantLoadingUtilsKt
-
Function to add a sequence Dictionary based on the reference genome. This uses the loaded genome to get the lengths.
- addStats(newCount, newNM, newAS, newDE, newStart) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- AddTaxaToTaxaGroupPlugin - Class in net.maizegenetics.pangenome.db_loading
-
- AddTaxaToTaxaGroupPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPlugin
-
- AddTaxaToTaxaGroupPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPlugin
-
- AddTaxaToTaxaGroupPluginKt - Class in net.maizegenetics.pangenome.db_loading
-
- addToAlt(position, hapIdInt) - Method in class net.maizegenetics.pangenome.hapCalling.PositionToRefAndAltHaplotypes
-
- addToCoordsMap(coordsFileRefToDataMap, line) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- addToRef(position, hapIdInt) - Method in class net.maizegenetics.pangenome.hapCalling.PositionToRefAndAltHaplotypes
-
- adjustEntryForOverlap(prevEntry, currentEntry, numOverlaps, snpByRefMap, snpByAsmMap, splitByRef) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
- adjustment(factor) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
-
- algorithmType() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
the type of algorithm. Choices are classic, which is
the original implementation describe by Rabiner 1989,
or efficient, which is modified for improved computational
efficiency.
- algorithmType(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Algorithm Type. the type of algorithm. Choices
are classic, which is the original implementation describe
by Rabiner 1989, or efficient, which is modified for
improved computational efficiency.
- alignChromsMultiThreaded(colsAndData) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
- alignDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- alignDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- alignGVCFDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- alignGVCFDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- AlignmentBlock(chromName, start, size, strand, chrSize, alignment) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- alignmentFiltered - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
-
- alignmentRaw - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
-
- AlignmentSummary(mappedReads, unmappedReads, minEditDistances) - Constructor for class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary
-
data class containing summary of alignment statstics for one file:
mappedReads: number of mapped reads
unmappedReads: number of unmapped reads
minEditDistances: list of the lowest edit distance for the alignments of each mapped read
Instead of printing the entire editDistances list, toString() calculates and prints mean and median
- alignWithNucmer(refFasta, asmFasta, outputDeltaFilePrefix, outputDir, mummer4Path, clusterSize) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Call mummer nucmer program to align the sequences Parameters are: -c 250: Set the minimum cluster length to 250 --mum: Use anchor matches that are unique in both the reference and query
- allCounts(state, anchor) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
-
- allCounts_oops(state, anchor) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
-
- allCountsWeighted(state, anchor) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
-
- AlleleInfo - Class in net.maizegenetics.pangenome.api
-
The AlleleInfo class holds the data for a record coming from the alleles tables in the PHG database.
- AlleleInfo(alleleId, baseStr, displayStr, len) - Constructor for class net.maizegenetics.pangenome.api.AlleleInfo
-
- allTaxonInstance(referenceSequence, vcfFileName, missingAsRef) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Method to get a map of taxon to its genome sequence for all the taxon in the vcf file
- altAllele() - Method in class net.maizegenetics.pangenome.api.Variant
-
- altAlleleID() - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- altAlleleString() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- altDepth() - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- alternativeSeqFile - Static variable in class net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
-
- AlterNucmerFirstLinePlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This method created to facilitate changing the first line of the mummer4 nucmer delta files.
When a new version of PHG db is being created, and it is using the same reference and
same assmebly fastas, the nucmer delta output can be used from the original alignment.
- AlterNucmerFirstLinePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
This method created to facilitate changing the first line of the mummer4 nucmer delta files.
When a new version of PHG db is being created, and it is using the same reference and
same assmebly fastas, the nucmer delta output can be used from the original alignment.
- AlterNucmerFirstLinePlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
This method created to facilitate changing the first line of the mummer4 nucmer delta files.
When a new version of PHG db is being created, and it is using the same reference and
same assmebly fastas, the nucmer delta output can be used from the original alignment.
- AlterNucmerFirstLinePluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- anchorBedFile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- anchorBedFileBase - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- anchorBedFileBaseDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- AnchorDataPHG - Class in net.maizegenetics.pangenome.db_loading
-
THis class differs from AnchorData in WGS_whatever as it includes more fields to match what is stored in PHGSchema's anchor_haplotypes. Specifically it includes ave_allele_depth and additional_data May 26, 2017: Class updated to include gene_start and gene_end These values needed when trimming anchors. The stored anchors have sequence of merged genes whose GFF start/end positions overlapped with 1000bp flanking on each end. THis 1000bp may be less is the distance between 2 genes is less than 2000bps.
- AnchorDataPHG(interval, asmContig, asmStart, asmEnd, asmStrand, gvcf, sequence, asmFileId, gvcfFileId) - Constructor for class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- anchorEnd() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
-
- anchorGFFFile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- anchorGFFFileBase - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- anchorGFFFileBaseDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- anchorId() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
-
- anchorIDFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
-
- anchorIDFile - Static variable in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
-
- AnchorInfo - Class in net.maizegenetics.pangenome.trimAnchors
-
Simple class which holds various information about an anchor. TODO formalize this datastructure Created by zrm22 on 6/8/17.
- AnchorInfo(anchorId, chrom, anchorStart, anchorEnd, geneStart, geneEnd) - Constructor for class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
-
- AnchorInfo(anchorId, chrom, anchorStart, anchorEnd, geneStart, geneEnd, leftTrimCount, rightTrimCount) - Constructor for class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
-
- anchorRegionBed() - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
-
Bed File
- anchorRegionBed(value) - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
-
Set Bed File. Bed File
- anchors() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Tab-delimited file containing Chrom, StartPosition, EndPosition
and Type
- anchors(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Set Anchors File. Tab-delimited file containing StartPosition, EndPosition
Type
- anchorStart() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
-
- anchorSummaryFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
-
- anchorSummaryFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
-
- anchorSummaryFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
-
- anchorwaveLocation() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Location of anchorwave on file system. This defaults
to use anchorwave if it is on the PATH environment
variable.
- anchorwaveLocation(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Set Location of anchorwave Executable. Location of
anchorwave on file system. This defaults to use anchorwave
if it is on the PATH environment variable.
- ancID() - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- answerDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- areGraphTaxaInRankingMap(graph, rankingMap) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
Method to verify that the taxa in the graph are in the ranking file. We can have more taxon in the ranking file than in the graph, but not the other way around.
- areRankingsUnique(rankingMap) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
Method to verify that rankings are unique. This is used to throw a Warning message in the Assembly consensus.
- areVariantInfosConsecutive(variantInfo1, variantInfo2) - Static method in class net.maizegenetics.pangenome.api.MergeVariantInfosKt
-
Simple method to check chromosome and positions to see if the infos are consective.
- asDNASequence() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- asmAligner() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
the aligner to use when processing assemblies. Choices
are mummer4, which is the original alignment, or anchorwave,
which has been shown to have higher quality alignment.
- asmAligner(value) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Set Asm Aligner. the aligner to use when processing
assemblies. Choices are mummer4, which is the original
alignment, or anchorwave, which has been shown to have
higher quality alignment.
- asmBZEnd() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
End position for bz region on the assembly
- asmBZEnd(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Set BZ Assembly End. End position for bz region on the assembly
- asmBZStart() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Start position for bz region on the assembly
- asmBZStart(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Set BZ Assembly Start. Start position for bz region on the assembly
- asmChr() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- asmContig() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
- asmContig() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- asmCSVdir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
Local directory to which the haplotype update CSV files
will be written.
- asmCSVdir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
Set Asm C S Vdir. Local directory to which the haplotype
update CSV files will be written.
- asmEnd() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
- asmEnd() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- asmEnd() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- asmFileId() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- asmKeyFile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- asmKeyFileDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- asmMAFKeyFile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- asmMAFKeyFileDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- asmPath() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
Path where assembly fastas live
- asmPath(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
Set Assembly Path. Path where assembly fastas live
- asmStart() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
- asmStart() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- asmStart() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- asmStrand() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
- asmStrand() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- asmStrand() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- ASMVariantInfo - Class in net.maizegenetics.pangenome.api
-
- ASMVariantInfo(asmChr, asmStart, asmEnd, asmStrand) - Constructor for class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- ASMVariantInfo() - Constructor for class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- assembly() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Assembly fasta file for a single chromosome to align against the reference
- assembly(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Set Assembly Fasta File. Assembly fasta file for a single chromosome to align against the reference
- assembly() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
Output fastq file to use as input for BWA-MEM
- assembly(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
Set Output File. Output fastq file to use as input for BWA-MEM
- AssemblyConsensusMetricPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This class takes a config file and list of methods. For each reference range ID,
it grabs from the haplotypes table the haplotypes_id, ref_range_id, gamete_grp_id, seq_len
and method_id for all entries with a method in the provided list.
- AssemblyConsensusMetricPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
This class takes a config file and list of methods. For each reference range ID,
it grabs from the haplotypes table the haplotypes_id, ref_range_id, gamete_grp_id, seq_len
and method_id for all entries with a method in the provided list.
- AssemblyConsensusMetricPluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- assemblyDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- assemblyDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- assemblyFasta() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Assembly fasta file used when aligning
- assemblyFasta(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Set Assembly Genome File. Assembly fasta file used when aligning
- AssemblyHaplotypesMultiThreadPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
Deprecated.
- AssemblyHaplotypesMultiThreadPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
This class runs mummer4 alignment of chrom-chrom fastas in a parallel fashion.
It expects a directory for both reference and assembly fastas, split by
chromosome, as well as a keyFile.
- AssemblyHaplotypesMultiThreadPlugin.InputChannelData - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
Deprecated.
- AssemblyHaplotypesMultiThreadPlugin.ResultChannelData - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
Deprecated.
- AssemblyHaplotypesMultiThreadPluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- AssemblyHaplotypesPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
Deprecated.
- AssemblyHaplotypesPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
- AssemblyHaplotypesPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
- AssemblyHaplotypesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
- AssemblyHaplotypesPlugin.ASSEMBLY_ENTRY_POINT - Enum in net.maizegenetics.pangenome.processAssemblyGenomes
-
Deprecated.
- AssemblyHapMetricPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This class creates a csv file of each reference range with the chr/start/end details, and
a column for each taxon. In each taxon's column is the length of the haplotype asociated with
that reference range. A 0 length means the haplotypes was not present for that taxon at that
reference range.
- AssemblyHapMetricPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
This class creates a csv file of each reference range with the chr/start/end details, and
a column for each taxon. In each taxon's column is the length of the haplotype asociated with
that reference range. A 0 length means the haplotypes was not present for that taxon at that
reference range.
- AssemblyHapMetricPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
This class creates a csv file of each reference range with the chr/start/end details, and
a column for each taxon. In each taxon's column is the length of the haplotype asociated with
that reference range. A 0 length means the haplotypes was not present for that taxon at that
reference range.
- AssemblyHapMetricPluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- assemblyKeyFile() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Key File for Assembly haplotypes.
- assemblyKeyFile(value) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Set Asm Key File. Key File for Assembly haplotypes.
- AssemblyMAFFromAnchorWavePlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This class creates MAF files of assembly genomes aligned to reference genomes
using the anchorWave program.
Details on anchorwave may be found here:
https://github.com/baoxingsong/AnchorWave
Input:
- AssemblyMAFFromAnchorWavePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
This class creates MAF files of assembly genomes aligned to reference genomes
using the anchorWave program.
Details on anchorwave may be found here:
https://github.com/baoxingsong/AnchorWave
Input:
- AssemblyMAFFromAnchorWavePlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
This class creates MAF files of assembly genomes aligned to reference genomes
using the anchorWave program.
Details on anchorwave may be found here:
https://github.com/baoxingsong/AnchorWave
Input:
- AssemblyMAFFromAnchorWavePlugin.InputChannelData - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- AssemblyMAFFromAnchorWavePluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- assemblyMethod() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Method name for the Assembly Based haplotypes being
uploaded.
- assemblyMethod(value) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Set Asm Method Name. Method name for the Assembly Based
haplotypes being uploaded.
- assemblyMethod() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Name to be stored to methods table for assembly method,
default is mummer4
- assemblyMethod(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Set Assembly Method Name. Name to be stored to methods
table for assembly method, default is mummer4
- assemblyMethod() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Method name to load to db for assembly processing, default is mummer4
- assemblyMethod(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Set Assembly Method. Method name to load to db for assembly processing, default is mummer4
- assemblyName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Name of Assembly Taxon, to be stored as taxon name in the DB
- assemblyName(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Set Assembly Name. Name of Assembly Taxon, to be stored as taxon name in the DB
- AssemblyProcessingUtils - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This class contains methods useful for processing assembly haplotypes.
- assemblyServerDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- AssemblyVariantInfo(chr, startPos, endPos, genotype, refAllele, altAllele, isVariant, alleleDepths, asmChrom, asmStart, asmEnd, asmStrand) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- asSequence() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- assignGenotpe(refAllele, altAllele, refDepth, altDepth) - Static method in class net.maizegenetics.pangenome.api.VariantUtils
-
- attemptToAddSAMRecordToBestReadMap(pairedEnd, currentSamRecord, readName, bestReadMap) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to try to add a SAM record to bestReadMap.
bestReadMap holds the currently best know set of reads which have the best(lowest) NM.
If the current Record is better, we replace the old entry with a new one.
If the current Record is the same, we add it to the list
If the current Record is worse, we ignore.
- augmentList(target, source) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MafUtils
-
target is a mutable list of maf records that are assumed to be sorted by chromosome and start. If there are
reference positions present in source that are absent from target then the sequence for those positions
will be added to target.
MAF start positions are 0-based numbers
- calcLevenshtein(seq1, seq2, maxEditDistance) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- calculate() - Method in class net.maizegenetics.pangenome.hapCalling.ViterbiForDiploidPath
-
- calculateCoordDistance(prev, current) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Calculates distance between 2 sets of mummer coords file entries This is called on coordinates that are both either ascending (start < end) or both descending (start > end) so "sign" of entries is not checked here.
- calculateDistanceMatrix(taxonToVariantInfoMap) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
-
- calculateFromHapSetCounts() - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- calculateLengthWeightedEmissionProbabilities() - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- calculateRegionCovered(asmCoveredMap, asmRange) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Given a map of ranges and a range, calculate the number of positions within the given range that are represented in the RangeMap.
- calculateWeightedExclusionCount(graph, node, readMap) - Static method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbabilityKt
-
- call() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
-
- callSNPsFromHaplotypeNodes(listOfNodes, hapIdToFileNameMapping, vcfFileDir, exportVCFFileName, referenceFileName, taxonName) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
- callSNPsFromHaplotypePath(graph, bestPath, vcfFileDir, exportVCFFileName, referenceFileName, taxonName) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
- callSNPsFromSomeVCFs(inputVCFFileDir, exportVCFFileName, referenceFileName, taxonName) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
- canVariantInfoBeAddedToRefBlockList(refBlocks, newVariantInfo) - Static method in class net.maizegenetics.pangenome.api.MergeVariantInfosKt
-
Function to check to see if a new variantInfo can be merged to the list of refBlocks.
- canVariantInfosBeMerged(variantInfoList) - Static method in class net.maizegenetics.pangenome.api.MergeVariantInfosKt
-
Method to determine if the list is able to be merged together.
- CentroidPathFromGraphPlugin - Class in net.maizegenetics.pangenome.hapcollapse
-
CentroidPathFromGraphPlugin calculates centroids from an input graph based on kmers from the HaplotypeNode sequence.
The id of the haplotype that is closest to the centroid for each reference range is stored as a path.
The path sequence can also be output to a fasta with one record per chromosome. In addition, a bedfile of reference range
coordinates can be written with the coordinates of the centroid genome.
- CentroidPathFromGraphPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
CentroidPathFromGraphPlugin calculates centroids from an input graph based on kmers from the HaplotypeNode sequence.
The id of the haplotype that is closest to the centroid for each reference range is stored as a path.
The path sequence can also be output to a fasta with one record per chromosome. In addition, a bedfile of reference range
coordinates can be written with the coordinates of the centroid genome.
- CentroidPathFromGraphPlugin() - Constructor for class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
CentroidPathFromGraphPlugin calculates centroids from an input graph based on kmers from the HaplotypeNode sequence.
The id of the haplotype that is closest to the centroid for each reference range is stored as a path.
The path sequence can also be output to a fasta with one record per chromosome. In addition, a bedfile of reference range
coordinates can be written with the coordinates of the centroid genome.
- ChangeDBMethodTypePlugin - Class in net.maizegenetics.pangenome.db_loading
-
This class allows a user to connect to a database and change the method type for an
entry in the PHG database methods table.
The original purpose of this plugin is to allow some methods to be marked as "test" methods
(based on DBLoadingUtils.METHOD_TYPE values). Then later, if they are considered good,
they can be converted to a more permanent type.
- ChangeDBMethodTypePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.ChangeDBMethodTypePlugin
-
This class allows a user to connect to a database and change the method type for an
entry in the PHG database methods table.
The original purpose of this plugin is to allow some methods to be marked as "test" methods
(based on DBLoadingUtils.METHOD_TYPE values). Then later, if they are considered good,
they can be converted to a more permanent type.
- ChangeDBMethodTypePluginKt - Class in net.maizegenetics.pangenome.db_loading
-
- changeFile(file, justFile, bw) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
- characteristics() - Method in class net.maizegenetics.pangenome.api.GraphSpliterator
-
- checkChrom2DupAnchor(refGenome) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- checkCoverage(idMap, currentPosition, minCoverage, windowSize, secondaryIdMap, secondaryIdMapMinCovCount) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function to check if the current window has high enough conservation. It will check >= minCoverage
- CheckDBVersionPlugin - Class in net.maizegenetics.pangenome.liquibase
-
This class connects to a data base, checks the db for the presense of specific
schema, and writes a file to the output directory indicating presence or absence of
the queried schema.
- CheckDBVersionPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin
-
This class connects to a data base, checks the db for the presense of specific
schema, and writes a file to the output directory indicating presence or absence of
the queried schema.
- checkForEmbedded(sortedList, splitByRef) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Check entries in a list of mummer4 coords file entries and removed those that are embedded
- checkForOverlap(prevStartEnd, curStartEnd) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Returns a Tuple indicating There will be inversions, so no guarantee prevStartEnd.x is <= curStartEnd.x
- checkForSeqMatch(idLine, shortSeq, assemblySequence) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
-
- checkNoListEntriesInRange(hashSet, testList) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Method takes a RangeSet of Integers and a list of integers. It returns "false" if any value from the list is present in the RangeSet It returns "true" if no value from the list is present in the RangeSet
- checkSnpEntryInRange(mline, coordsRangeMap, chrom) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Verifies if the positions from a Mummer4 snp file fall within the range map of reference and assembly positions created from the Mummer4 coordinates files.
- chooseVarIdForSNPPositionFromGenotypeTable(genotypeTable, posCallVarIdMap) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
- chrom() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
If a chrom is specified, pull only data for that chromosome. If no chromosome is specified, data for all chromsomes will be pulled.
- chrom(value) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
Set Chrom. If a chrom is specified, pull only data for that chromosome. If no chromosome is specified, data for all chromsomes will be pulled.
- chrom() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Name of chromosome as it appears both for the reference in the db reference_ranges table, and in the fasta file idLine for the assembly
- chrom(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Set Chromosome Name. Name of chromosome as it appears both for the reference in the db reference_ranges table, and in the fasta file idLine for the assembly
- chrom() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
-
- chromLengthLookup - Variable in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- chromosome() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- chromosome() - Method in class net.maizegenetics.pangenome.api.ReferenceRange
-
Chromosome in the reference genome from which this ReferenceRange originates
- chromosome() - Method in class net.maizegenetics.pangenome.api.Variant
-
- ChromosomeGVCFRecord(currentChrom, currentTaxon, gameteId, anchorDataMapping, ghd, asmServerPath, asmLocalPath, gvcfServerPath, localGVCFFile) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- ChromosomeGVCFRecord(currentChrom, currentTaxon, anchorDataMapping) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin.ChromosomeGVCFRecord
-
- chromosomes() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
- chromosomes() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Chromosomes
- chromosomes(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Set Chromosomes. Chromosomes
- chromosomes() - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- chromosomes - Variable in class net.maizegenetics.pangenome.pipelineTests.RefRangeVectors
-
- chromosomeSequence(chrom) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
Unsupported method to get the sequence for the whole chromosome
- chromosomeSequence(chrom, startSite, endSite) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
- chromosomeSequence(chrom) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- chromosomeSequence(chrom, startSite, endSite) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- chromosomeSize(chromosome) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- classicAlgorithm() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Use the classic algorithm to compute the Viterbi algorithm
as described in Rabiner 1989. Significantly slower
than the default algorithm.
- classicAlgorithm(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Classic Algorithm. Use the classic algorithm to
compute the Viterbi algorithm as described in Rabiner
- clear() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdMultiset
-
Method to clear out the multiset and create a new empty one.
- client - Variable in class net.maizegenetics.pangenome.io.SFTPConnection
-
- close() - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- close() - Method in class net.maizegenetics.pangenome.io.SFTPConnection
-
Function to automatically close out this class so it can be used in a .use{} code block.
- CloseDBConnectionPlugin - Class in net.maizegenetics.pangenome.db_loading
-
This method closes a DB connection. The connection is expected as part of the input DataSet parameter set.
- CloseDBConnectionPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
-
- CloseDBConnectionPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
-
- CloseDBConnectionPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
-
- closeGVCFfileReaders(gvcfIdToVCFReader) - Static method in class net.maizegenetics.pangenome.api.VariantUtils
-
Closes all open VCFFileReaders for the input list.
- clusterAssemblies() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
-
Method to cluster Assemblies Steps Taken Here: For the current Reference Range, extract out all haplotypes in the graph Compute a distance matrix using #SNPS/(#SNPs+#Ref) as the distance. Ignore indels and Ns. From this distance matrix, compute a UPGMA tree and cut at parameter mxDiv Within each sub group, chose a single haplotype to be the representative haplotype. This choice is done by the external rankingFile required to run this Once the representative haplotypes are chosen, write them to the db with the full Taxa list for the sub-group
- clusteringMode() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Clustering mode
- clusteringMode(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Clustering Mode. Clustering mode
- clusterMethod() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
The method used to cluster taxa. Coverage seeds the first cluster with the highest coverage taxon. UPGMA builds a UPGMA tree then cuts it at maxDistance.
- clusterMethod(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Cluster Method. The method used to cluster taxa. Coverage seeds the first cluster with the highest coverage taxon. UPGMA builds a UPGMA tree then cuts it at maxDistance.
- clusterMethod() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
The method used to cluster taxa. Coverage seeds the first cluster with the highest coverage taxon. UPGMA builds a UPGMA tree then cuts it at maxDistance.
- clusterMethod(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Set Cluster Method. The method used to cluster taxa. Coverage seeds the first cluster with the highest coverage taxon. UPGMA builds a UPGMA tree then cuts it at maxDistance.
- clusterSize() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Cluster size to use with mummer4 nucmer script.
- clusterSize(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Set Mummer4 Nucmer Cluster Size . Cluster size to use
with mummer4 nucmer script.
- clusterSize() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Cluster size to use with mummer4 nucmer script.
- clusterSize(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Set Mummer4 Nucmer Cluster Size . Cluster size to use with mummer4 nucmer script.
- clusterThenMerge() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
-
- collapseMethod() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Name of the collapse method to be stored in the database
- collapseMethod(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Set Collapse Method. Name of the collapse method to be stored in the database
- collapseMethod() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Name of the collapse method to be stored in the database
- collapseMethod(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Collapse Method. Name of the collapse method to be stored in the database
- collapseMethodDetails() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Details for the collapse method to be stored in the database
- collapseMethodDetails(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Set Collapse Method Details. Details for the collapse method to be stored in the database
- collapseMethodDetails() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Details for the collapse method to be stored in the database
- collapseMethodDetails(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Collapse Method Details. Details for the collapse method to be stored in the database
- columnNames - Variable in class net.maizegenetics.pangenome.api.RMethods.DataFrameVectors
-
- columnNames - Variable in class net.maizegenetics.pangenome.api.RMethods.MatrixWithNames
-
- command() - Method in class net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin
-
Command for liquibase to execute: must be update or
changeLogSync, defaults to update.
- command(value) - Method in class net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin
-
Set Liquibase command. Command for liquibase to execute:
must be update or changeLogSync, defaults to update.
- command() - Method in class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPlugin
-
Liquibase command to run
- command(value) - Method in class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPlugin
-
Set Command. Liquibase command to run
- Companion - Static variable in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
- comparaRawFilteredAlignment(inMSA, outMSA) - Static method in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
-
- ComparatorTriple - Class in net.maizegenetics.pangenome.pipeline
-
- ComparatorTriple() - Constructor for class net.maizegenetics.pangenome.pipeline.ComparatorTriple
-
- compare(o1, o2) - Method in class net.maizegenetics.pangenome.pipeline.ComparatorTriple
-
- CompareAssembliesToReference - Class in net.maizegenetics.pangenome.hapcollapse
-
Simple little utility to compare assembly alignments to the reference genome
- compareEdges(edges1, edges2) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
- CompareFastaToReference - Class in net.maizegenetics.pangenome
-
Created by terry on 3/21/17.
- CompareHaplotypesToAssembly - Class in net.maizegenetics.pangenome
-
Created by terry on 3/21/17.
- compareKmerLoop(kmerArray, refRangeIdArray, purgeArray, mask, minAllowedHammingDist, kmerRefRangePurgeSwapper) - Static method in class net.maizegenetics.pangenome.hapCalling.KmerUtils
-
Function critical to run the hamming distance comparison.
- compareRefToReAssembledChrom(refGenome, reAssembledChromFasta, chrom, coordinatesFile, outputFile) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- compareTo(o) - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
- compareTo(o) - Method in class net.maizegenetics.pangenome.api.ReferenceRange
-
- compareTo(other) - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- compareTo(that) - Method in class net.maizegenetics.pangenome.db_loading.GeneGFFData
-
- compareTo(other) - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- compareTo(other) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.VariantInfoConsensus
-
- compareTo(compareFruit) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- CompareToKnownSNPPlugin - Class in net.maizegenetics.pangenome.pipelineTests
-
Plugin to compare A GenotypeTable to a known trusted GenotypeTable Inputs: -DataSet of at least 2 GenotypeTables, First one is the known SNP set you wish to compare to, the rest are compared in order. -bedFile, bed file of regions you want to compare. If not specified will compare all base pairs in the known SNP set Outputs: - Will print out the Number of HetIndelMissing base pairs, the number of missing base pairs, the number of base pairs compared and the error rate to the console. Created by zrm22 on 12/18/17.
- CompareToKnownSNPPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
-
- component1() - Method in class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- component1() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin.RefrangeInfo
-
- component1() - Method in class net.maizegenetics.pangenome.api.Method
-
- component1() - Method in class net.maizegenetics.pangenome.api.RPHGMethodsKotlin.HaplotypeSequences
-
- component1() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- component1() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingInput
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingInput
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdSetCount
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.KmerToRefRangeIdToPurgeArray
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin.ReadMappingResult
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.SecondaryStats
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.SingleHapMapping
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component1() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- component1() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileInput
-
- component1() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileResult
-
- component1() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- component1() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- component1() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- component1() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- component1() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.ResultChannelData
-
Deprecated.
- component1() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- component1() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.RefRangeData
-
- component1() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.UpdateData
-
- component1() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin.ChromosomeGVCFRecord
-
- component1() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- component1() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component1() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.MAFRecord
-
- component10() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component10() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component10() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- component10() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component11() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component11() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component11() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component12() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component12() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component13() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component14() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component15() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component16() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component17() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component18() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component2() - Method in class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- component2() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin.RefrangeInfo
-
- component2() - Method in class net.maizegenetics.pangenome.api.Method
-
- component2() - Method in class net.maizegenetics.pangenome.api.RPHGMethodsKotlin.HaplotypeSequences
-
- component2() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- component2() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingInput
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingInput
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdSetCount
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.KmerToRefRangeIdToPurgeArray
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin.ReadMappingResult
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.SecondaryStats
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.SingleHapMapping
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component2() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- component2() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileInput
-
- component2() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileResult
-
- component2() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- component2() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- component2() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- component2() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- component2() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.ResultChannelData
-
Deprecated.
- component2() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- component2() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.RefRangeData
-
- component2() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.UpdateData
-
- component2() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin.ChromosomeGVCFRecord
-
- component2() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- component2() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component2() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.MAFRecord
-
- component3() - Method in class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- component3() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin.RefrangeInfo
-
- component3() - Method in class net.maizegenetics.pangenome.api.Method
-
- component3() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- component3() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.KmerToRefRangeIdToPurgeArray
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin.ReadMappingResult
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.SecondaryStats
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component3() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- component3() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- component3() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- component3() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- component3() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- component3() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.ResultChannelData
-
Deprecated.
- component3() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- component3() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.RefRangeData
-
- component3() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.UpdateData
-
- component3() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin.ChromosomeGVCFRecord
-
- component3() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- component3() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component3() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.MAFRecord
-
- component4() - Method in class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- component4() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- component4() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- component4() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- component4() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- component4() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- component4() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component4() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- component4() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- component4() - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- component4() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- component4() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component4() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- component4() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- component4() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- component4() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- component4() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- component4() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- component4() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.UpdateData
-
- component4() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- component4() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component5() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- component5() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- component5() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- component5() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component5() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- component5() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- component5() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- component5() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component5() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- component5() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- component5() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- component5() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- component5() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- component5() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component6() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- component6() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- component6() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- component6() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component6() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- component6() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- component6() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component6() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- component6() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- component6() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- component6() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- component6() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- component6() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component7() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- component7() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component7() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component7() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- component7() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- component7() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component8() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- component8() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component8() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component8() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- component8() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- component8() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- component9() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- component9() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- component9() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- component9() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- component9() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- component9() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- compress(str) - Static method in class net.maizegenetics.pangenome.db_loading.GZipCompression
-
- compress(bytes) - Static method in class net.maizegenetics.pangenome.db_loading.GZipCompression
-
- computeDepths(variants) - Static method in class net.maizegenetics.pangenome.api.MergeVariantInfosKt
-
- computeKmerCounts(sequence, kmerSize) - Static method in class net.maizegenetics.pangenome.hapcollapse.KmerBasedConsensusUtils
-
Counts the Kmers (of kmerSize) for the given Haplotype
- computeKmerEuclideanDist(kmerMap1, kmerMap2, divisor) - Static method in class net.maizegenetics.pangenome.hapcollapse.KmerBasedConsensusUtils
-
Computes Kmer distance based on Euclidean formula
- computeKmerEuclideanDistToCentroid(centroid, kmerMap, divisor) - Static method in class net.maizegenetics.pangenome.hapcollapse.KmerBasedConsensusUtils
-
Computes Kmer distance based on Euclidean formula for distance to a centroid.
Similar to distance calculation between two kmer maps, except the centroid has doubles for scores.
- computeKmerManhattanDist(kmerMap1, kmerMap2, divisor) - Static method in class net.maizegenetics.pangenome.hapcollapse.KmerBasedConsensusUtils
-
Computes Kmer distance based on Manhattan formula
- ComputeMedianAnnotation - Class in net.maizegenetics.pangenome.gvcfFiltering
-
Simple Utility to Extract Mean, Median and Mode for Depth in a GVCF file Currently supports only DP as defined in the FORMAT Tag. If the value is missing, it will not count anything. For a reference block, it will count the depth for each base pair in the block. For a variant, it will count the depth once. Created by zrm22 on 6/30/17.
- ComputeMedianGVCFAndFilter - Class in net.maizegenetics.pangenome.gvcfFiltering
-
TODO Separate Filter from FastaExtraction Created by zrm22 on 7/18/17. This class will filter a GVCF file based on user specified criteria and will export both the filtered GVCF and the fasta setquence that the DB loader expects. The user can provide the specified criteria using a config file(similar to db configs and the class will filter. Alternatively, the user can provide an upper and lower bound for poisson-based depth filtering. The following options are currently valid for filtering: exclusionString = String used for bcftools filtering. If this is specified, no additional terms are added to exclude DP_poisson_min = minimum poisson bound used for filtering(absolute minimum is 0.0) DP_poisson_max = maximum poisson bound used for filtering(absolute maximum is 1.0) DP_min = minimum DP bound DP_max = maximum DP bound GQ_min = minimum GQ bound GQ_max = maximum GQ bound QUAL_min = base quality minimum bound QUAL_max = base quality maximum bound filterHets = true/false or t/f, if true will filter sites where 2 or more alleles have above 0 AD
- ComputeNDistribution - Class in net.maizegenetics.pangenome.multiSequenceAlignment
-
Simple One off Main class to compute how many Ns we have over all the basepairs of all the anchors TODO if needed in pipeline, Refractor into TASSEL code Created by zrm22 on 5/25/17.
- configFile() - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
Config file containing lines for host=,user=, password=,
DB= and DBtype= where DBtype is either sqlite or postgres.
- configFile(value) - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
Set Config File. Config file containing lines for host=,user=,
password=, DB= and DBtype= where DBtype is either sqlite
or postgres.
- configFile() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Database configuration file
- configFile(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Set Database Config File. Database configuration file
- configFile() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
Database configuration file
- configFile(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
Set Config File. Database configuration file
- configFile(filename) - Method in class net.maizegenetics.pangenome.api.MethodTableReportPlugin
-
- configFile() - Method in class net.maizegenetics.pangenome.api.MethodTableReportPlugin
-
- configFile() - Method in class net.maizegenetics.pangenome.api.ReadMethodTablePlugin
-
- configFile(filename) - Method in class net.maizegenetics.pangenome.api.ReadMethodTablePlugin
-
- configFile() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
Path to config file for db loading
- configFile(value) - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
Set config file for db access
- configFile() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
Path to file containing database access information, separate lines for host=X, user=X, password=X, DB=X, DBtype=X where X is user defined, and DBtype is either sqlite or postgres.
- configFile(value) - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
Set DataBase Configuration File. Path to file containing database access information, separate lines for host=X, user=X, password=X, DB=X, DBtype=X where X is user defined, and DBtype is either sqlite or postgres.
- configFile() - Method in class net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin
-
Configuration file
- configFile(value) - Method in class net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin
-
Set Config File. Configuration file
- configFile() - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
- configFile(value) - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
Set DB Config Files. File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
- configFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
Config folder containing the filtering parameters.
- configFile(value) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
Set Config File. Config folder containing the filtering parameters.
- configFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
Config folder containing the filtering parameters.
- configFile(value) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
Set Config File. Config folder containing the filtering parameters.
- configFile() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
Config file that specifies database connection parameters
- configFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
Set Config File. Config file that specifies database connection parameters
- configFile() - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
File containing lines with data for host=, user=, password=
and DB=, DBtype= used for db connection
- configFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
Set DB Config File. File containing lines with data
for host=, user=, password= and DB=, DBtype= used for
db connection
- configFile() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Database configuration file
- configFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Set Database Config File. Database configuration file
- configFile() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Database configuration file
- configFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Set Config File. Database configuration file
- configFile() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Database configuration file
- configFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Set Database Config File. Database configuration file
- configFile() - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
Database configuration file
- configFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
Set Config File. Database configuration file
- configFile() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
The config file name.
- configFile(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Config File. The config file name.
- configFile() - Method in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
-
Config file that specifies database connection parameters
- configFile(value) - Method in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
-
Set Config File. Config file that specifies database connection parameters
- configFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
FIle with infor for database access
- configFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
Set Config File. FIle with infor for database access
- configFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
FIle with infor for database access
- configFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
Set Config File. FIle with infor for database access
- configFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
Config file with paraeters for database connection.
- configFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
Set Config File. Config file with paraeters for database
connection.
- configFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
- configFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Set DB Config File. File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
- configFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
- configFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Set DB Config File. File containing lines with data for host=, user=, password= and DB=, DBtype= used for db connection
- configFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
Config file with database connection information
- configFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
Set Config File. Config file with database connection
information
- configFileForFinalDB() - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
File containing lines with data for host=, user=, password=
and DB=, DBtype= used for db connection
- configFileForFinalDB(value) - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Set Final DB Config File. File containing lines with
data for host=, user=, password= and DB=, DBtype= used
for db connection
- connection(propertiesFile) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Creates a database connection given a properties file
- connection(host, user, password, dbName) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Creates a sqlite database connection.
- connection(createNew) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
Creates a database connection from the TASSEL ParameterCache It is expected that only initial db loading methods will call this with "createNew" = true.
- connection(propertiesFile, createNew) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
Creates a database connection given a properties file It is expected that only initial db loading methods will call this with "createNew" = true.
- connection(host, user, password, dbName, type, createNew) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
Creates a new database connection or returns connection to existing db If createNew is FALSE then try to connect, and if db doesn't exist, return NULL NOTE: from postgres, User should never create a db that matches all lower case to an existing db. This will cause errors as our db check verifies based on all-lower case. To get a camel-case db name, the db must be created and accessed using This is likely to cause confusion, so this code defaults to postgres all-lowercase db names.
- consensusFastaOutputDir() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Directory where you want to store the output fastas from the consensus process
- consensusFastaOutputDir(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Set Consensus Fasta Output Dir. Directory where you want to store the output fastas from the consensus process
- consensusHaplotypes - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
-
- consensusMethod() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Method name for the Consensus being uploaded.
- consensusMethod(value) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Set Consensus Method Name. Method name for the Consensus
being uploaded.
- ConsensusProcessingUtils - Class in net.maizegenetics.pangenome.hapcollapse
-
This class holds methods for processing consensus using the variants and alleles tables or data derived from them.
- consensusVariants(taxonToVariantInfoMap, taxa, refRange) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
-
- consensusVCFOutputDir() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Directory where you want to store the output VCFs from the consensus process
- consensusVCFOutputDir(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Set Consensus VCF Output Dir. Directory where you want to store the output VCFs from the consensus process
- conservedGeneFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
File containing list of conserved genes to include as anchor regions
- conservedGeneFile(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
Set Conserved Gene File. File containing list of conserved genes to include as anchor regions
- contigBAM() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
Name of contig BAM file to process
- contigBAM(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
Set Contig File. Name of contig fasta file to process
- ContrastHaplotypeAndAssemblySequence - Class in net.maizegenetics.pangenome.pipelineTests
-
Integration test to evaluate fasta file generated from GVCF files for the whole genome against assembly fasta Assembly fasta Read B73 reference sequences for IBD anchors Read fasta file obtained with the practical haplotype pipeline (W22). Read fasta file obtained from assembly (W22). Power: how many of the anchor perfectly match the assembly reference? Question: how frequently assembly and anchor region diverge? Created by mm2842 on 6/23/17.
- convertAllFiles() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
Set up multithreading and hand out files to each thread
- convertContextToInfo(variantContext, gameteId) - Static method in class net.maizegenetics.pangenome.api.ConvertVariantContextToVariantInfo
-
Function to convert a VariantContext into a VariantInfo object.
Need taxon and gamete id to get the correct genotype from the VariantContext.
The gamete ID is used to get the correct allele for the genotype.
- convertCSVToBed(args) - Static method in class net.maizegenetics.pangenome.ConvertToHaplotypeCallerInput
-
- convertCSVToIntervals(args) - Static method in class net.maizegenetics.pangenome.ConvertToHaplotypeCallerInput
-
- convertFile(file) - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
Write a fasta or a fastq file from the given FASTQCOL input file
- convertGVCFContextToInfo(variantContext, gameteId) - Static method in class net.maizegenetics.pangenome.api.ConvertVariantContextToVariantInfo
-
- convertGVCFListToVariantInfoList(variants, gameteId) - Static method in class net.maizegenetics.pangenome.api.ConvertVariantContextToVariantInfo
-
- convertGVCFRemoteToLocalFiles(gvcfIdToRemotePath, localGVCFFolder) - Static method in class net.maizegenetics.pangenome.api.VariantUtils
-
takes the remote gvcf file paths as stored in the db genome_file_data table, and translates them to a local path based on the user provided localGVCFFolder value
- convertHitMapToSingleHapMapping(readNames, bestHitMap, hapIdToRangeMap, filterFunction, mapToListFunction) - Static method in class net.maizegenetics.pangenome.hapCalling.ReadMappingUtils
-
Function to do some filtering on read mappings then will convert the mappings into the correct datastructure for the multimaps
- convertLine(oldLine) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
- convertMethods(methodPairs) - Static method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
- convertMethods(methodPairs) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin.Companion
-
- convertMethodsToList(methods) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPluginKt
-
- ConvertRampSeqTagsToMapPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Created by zrm22 on 10/4/17.
- ConvertRampSeqTagsToMapPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
- ConvertReadsToPathUsingHMM - Class in net.maizegenetics.pangenome.hapCalling
-
- ConvertReadsToPathUsingHMM() - Constructor for class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- ConvertToHaplotypeCallerInput - Class in net.maizegenetics.pangenome
-
- ConvertVariantContextToVariantInfo - Class in net.maizegenetics.pangenome.api
-
- convertVariantInfoToContext(sampleName, variantInfo) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Function to turn the AssemblyVariantInfo into an actual VariantContext.
If the Assembly annotations are not in the VariantInfo, we do not add them into the VariantContext.
- convertVariantsToSequence(variants, refRange, refSequence) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
- convertVCFToGVCF(vcfVariantContexts) - Static method in class net.maizegenetics.pangenome.hapcollapse.GVCFUtils
-
- convertVCListToVariantInfoList(variants, taxon, gameteId) - Static method in class net.maizegenetics.pangenome.api.ConvertVariantContextToVariantInfo
-
Function to convert a list of variantContexts into a list of VariantInfos
- coordsFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Output of Mummer coords file
- coordsFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Set Mummer Coords File. Output of Mummer coords file
- coordsFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Output of Mummer coords file
- coordsFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Set Mummer Coords File. Output of Mummer coords file
- copy(asmChr, asmStart, asmEnd, asmStrand) - Method in class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- copy(chr, start, end) - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin.RefrangeInfo
-
- copy(name, id, type) - Method in class net.maizegenetics.pangenome.api.Method
-
Data class for holding row from the PHG methods table.
- copy(hapId, sequence) - Method in class net.maizegenetics.pangenome.api.RPHGMethodsKotlin.HaplotypeSequences
-
Data class for storing haplotype ID / sequence strings
- copy(currentChrom, currentTaxon, gameteId, anchorDataMapping, ghd, asmServerPath, asmLocalPath, gvcfServerPath, localGVCFFile) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- copy(methodName, methodDetails, readMappingId, readMappings, genoName, fileGroupName) - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- copy(readName, strand, bestEditDistance, lengthOfMapping, listOfHapIds, hapIdToSecondaryStats) - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- copy(keyFileEntry, readMappingCounts) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingInput
-
- copy(keyFileEntry, path, likelyParents, totalReads) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- copy(keyFileEntry, readMappingCounts) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingInput
-
- copy(keyFileEntry, path, likelyParents, totalReads) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- copy(refRangeId, numReads, totalReadBps, totalAlignedBps, totalNM, totalSClip, totalHClip, totalEQ, totalX, totalI, totalD) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- copy(hapIdToRefRangeMap, hapIdToLengthMap, refRangeToHapIdMap, haplotypeListId, hapIdToTaxaList) - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
Class to hold the 4 pieces of information which are needed for readMapping.
Using Jackson this class can be serialized into JSON
- copy(hapIdSet, count) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdSetCount
-
- copy(hapId, count, NM, AS, de, startPositions) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- copy(methodName, taxonName, fileGroupName) - Method in class net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord
-
- copy(kmerArray, refRangeIdArray, purgeArray) - Method in class net.maizegenetics.pangenome.hapCalling.KmerToRefRangeIdToPurgeArray
-
Simple data class to hold the three arrays.
- copy(keyFileRecord, hapIdMultiset, hapIdToStatMap) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin.ReadMappingResult
-
- copy(keyFileRecordsToFileMap, fileNameToPathMap, keyFileColumnNameMap, keyFileLines) - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- copy(myReferenceName, myChromosome, myStart, myEnd, myID, myMethods) - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
Need a ReferenceRange Wrapper function as the Current ReferenceRange is not serializable due to the Chromosome object.
- copy(mappedReads, unmappedReads, minEditDistances) - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary
-
data class containing summary of alignment statstics for one file:
mappedReads: number of mapped reads
unmappedReads: number of unmapped reads
minEditDistances: list of the lowest edit distance for the alignments of each mapped read
Instead of printing the entire editDistances list, toString() calculates and prints mean and median
- copy(AS, de, startPosition) - Method in class net.maizegenetics.pangenome.hapCalling.SecondaryStats
-
- copy(readName, hapIdSet) - Method in class net.maizegenetics.pangenome.hapCalling.SingleHapMapping
-
- copy(numIndels, meanIndel, indelLowerQuartile, indelMedian, indelUpperQuartile, indelLargest, numIns, meanIns, insLowerQuartile, insMedian, insUpperQuartile, insLargest, numDel, meanDel, delLowerQuartile, delMedian, delUpperQuartile, delLargest) - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
Data class containing summary information about indel distribution (number of insertions/deletions, average sizes, etc.)
toString() is overridden in order to make printing to tab-delimited summary file easier
- copy(name, numSNPs, numIndels, basesAligned, basesInserted, basesDeleted, basesGapped, totalBases, indelSizes) - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
Data class containing summary statistics for a particular file or contig/chromosome
- copy(refRange, nodeList) - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileInput
-
- copy(refRange, pairList) - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileResult
-
- copy(start, end, count, type) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- copy(start, end, type, variantContextMap) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- copy(queryName, refName, totalEQ, totalSNP, totalM, totalInserts, totalDeletes, editDistance, totalReadLength, totalRefLength) - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- copy(refFasta, asmFasta, asmDBName, chrom, asmServer, asmFullGenomeFasta) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- copy(IdToRefRangeMap, vcList, fastaInfo) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.ResultChannelData
-
Deprecated.
- copy(refFasta, asmFasta, asmDBName, outputDir, gffFile, refSamOutFile) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- copy(chrom, start, end) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.RefRangeData
-
- copy(id, asmStart, asmEnd, asmStrand) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.UpdateData
-
- copy(currentChrom, currentTaxon, anchorDataMapping) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin.ChromosomeGVCFRecord
-
- copy(chromName, start, size, strand, chrSize, alignment) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- copy(chr, startPos, endPos, genotype, refAllele, altAllele, isVariant, alleleDepths, asmChrom, asmStart, asmEnd, asmStrand) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- copy(score, refRecord, altRecord) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.MAFRecord
-
- copyGvcfsToLocalDir(localDownloadDir) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Function to take the gvcf files used for storing assemblies and wgs,
and copy them to the folder used for downloading gvcf files from the server.
It is expected that when users run each step of the pipeline separately,
they will download the files needed. When running the steps through
PopulatePHGDBPipelinePlugin, the code will need to download these files
before consensus can be run (e.g. for smallSeq)
- count(hapIds) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdMultiset
-
Method to return the count for a given hapId set. We sort the hapId set again just to be safe.
- countAD() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Use the Allele Depths as the counts for the Read Mappings
instead of SNPs
- countAD(value) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Set Count Allele Depths. Use the Allele Depths as the
counts for the Read Mappings instead of SNPs
- countDistinctID(gffSet, contig) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Counts the number of distinct ID values either across the full
GFF3Feature set (if contig==null) or for a specific contig
- countFiles($receiver) - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
load file indices to channel
- countMethod() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
The haplotype count method name assigned when the counts were created and stored in the DB. Not required if a path file name is supplied or if only one method was used to find a path for this taxon.
- countMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Set Haplotype count method name. The haplotype count method name assigned when the counts were created and stored in the DB. Not required if a path file name is supplied or if only one method was used to find a path for this taxon.
- countNsInFasta() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- CountNsInRawHapSequencesPlugin - Class in net.maizegenetics.pangenome.pipelineTests
-
Deprecated.
- CountNsInRawHapSequencesPlugin() - Constructor for class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
- CountNsInRawHapSequencesPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
- CountNsInRawHapSequencesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
- countRegionHaplotypes(start, end, taxonVcMap, refGenome, mxDiv) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function that counts the number of haplotype clusters in a region
- countsFromHapidList(hapidList) - Static method in class net.maizegenetics.pangenome.hapCalling.FindBestDiploidPathKt
-
- coverage() - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
average coverage of reads for a reference range
- coverage(value) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
Set Coverage. average coverage of reads for a reference
range
- coverageListToCoveredRanges(coverageList, windowSize, minCoverage) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Converts
coverageList, which is a ordered list of coverage for individual positions, to a RangeSet of sites
meeting the coverage criterion specified by minCoverage and windowSize. All positions in the range
have coverage >= minCoverage and are bordered by a minimum of windowSize sites on either side that also meet
that are covered.
- create(lengthOfGenes, lengthOfInterGenes, proportionOfRefInterGeneDuplicated, proportionOfInterGeneDeleted, numberOfGenes, lengthOfReads, haplotypeDivergence, intraHaplotypeDivergence, wgsDepth, gbsDepth, insertProportion) - Static method in class net.maizegenetics.pangenome.smallseq.CreateTestGenomes
-
- createAlleleList(vc) - Static method in class net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
-
createALleleList returns an array list containing just the ref allele string, if the VariantContext record is a ref record. Or both the ref allele and first alt allele, if the VariantContext record is a variant record. THis method does not check if the allele exists. The returned list is ALL alleles - this assumes they will be added via an INSERT/IGNORE db command.
- createAlleleList(vi) - Static method in class net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
-
Method to create a list of alleles based on if the variant info is a ref or variant.
- CreateAnchorFilesFromGeneGFF - Class in net.maizegenetics.pangenome.db_loading
-
Based on WGS_whatever.CreateAnchorsFromGeneGff.java This method creates two fasta files of anchor coordinates: The first has exact gene coordinates to be used when blasting B73 reference genes against a particular assembly, e.g. Sorghum. The second has genes with 1000bp flanking added. Method: Takes a gff file sorted to contain only gene data If any gene is embedded within another, it is tossed. If any gene start position overlaps the previous gene end position, merge the gene. After mergin genes, add 1000bp flanking on either end. If there is less than 2000 bps between genes, spli the difference Can take 1 file or a directory of files. The file names are assume to look like this: gffv4Rel34_chr5_gene.txt This matters to the parsing of the chromosome name (ie "5" above) OUTPUT Notes: 1. Two csv files of chr,start,end are created for each chromosome. The first has just merged/tossed gene coordinates, the second has these genes with 1000bp flanking added. 2. A fasta file for each chromosome is created: contains all the anchors for that chromosome. This was created when the thought was that Zack needed it for comparison. THis way he didn't have to go through a db. 3. The fasta files are not used in LoadAnchorsToPHGdb.java. It uses the csv file created which contains that chr,start,end. They ARE used when blasting genes against the assemblies. 4. AFter all the chromosomes have been processed, concat them into 1 file for use with LoadANchorsToPHGdb.java via this command line: cat anchorsFile_chr1_MergedPlus1000orGapDiffcoordinates.csv anchorsFile_chr2_MergedPlus1000orGapDiffcoordinates.csv ... > anchorsFile_all10_MergedPlus1000orGapDiffcoordinates.csv - Then edit out the header lines except for the first one.
- createAndLoadAssemblyData(idByRangeMap, fullVC, refSequence, dbConn, assemblyName, chrom, clusterSize, method, pluginParams) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Create the assembly genotype/haplotype data and load to the PHG database
- createAndWriteHapIdMaps(hapIdToRefRangeMap, hapIdToLengthMap, refRangeToHapIdMap, haplotypeListId, hapIdToTaxaListMap, outputFileName) - Method in class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
- createASMAnchorWaveHaplotypes(gvcfServerPath) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
function to create assembly haplotypes with anchorwave as the aligner.
It runs anchorwave, converts the anchorwave MAF files to GVCF Files,
then calls the LoadHaplotypesFromGVCFPlugin to load the assembly data.
- createAsmCoordinatesRangeMap(refCoords) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Creates a RangeMap of asm positions from the given reference range map, using lower reference position as the value.
- CreateASMCoordsUpdateFilesPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This class traverses the db and writes, to csv files, the haplotypes_id, asm_start_coordinate, asm_end_coordinate,
asm_strand values. These files will be loaded to the db into a temp table, from which updates will occur for haplotype
nodes. This class is a successor to UpdateDBAsmCoordinatesPlugin.kt. There were issues with batching
in the original class - only single updates, one at a time, worked.
- CreateASMCoordsUpdateFilesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
This class traverses the db and writes, to csv files, the haplotypes_id, asm_start_coordinate, asm_end_coordinate,
asm_strand values. These files will be loaded to the db into a temp table, from which updates will occur for haplotype
nodes. This class is a successor to UpdateDBAsmCoordinatesPlugin.kt. There were issues with batching
in the original class - only single updates, one at a time, worked.
- CreateASMCoordsUpdateFilesPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
This class traverses the db and writes, to csv files, the haplotypes_id, asm_start_coordinate, asm_end_coordinate,
asm_strand values. These files will be loaded to the db into a temp table, from which updates will occur for haplotype
nodes. This class is a successor to UpdateDBAsmCoordinatesPlugin.kt. There were issues with batching
in the original class - only single updates, one at a time, worked.
- CreateASMCoordsUpdateFilesPlugin.RefRangeData - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- CreateASMCoordsUpdateFilesPlugin.UpdateData - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- CreateASMCoordsUpdateFilesPluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- createASMHaplotypes() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Function to create Assembly based Haplotypes.
- CreateBiggerIntervals - Class in net.maizegenetics.pangenome.db_loading
-
- createCDSfromRefData(refFasta, gffFile, cdsFasta, outputDir) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
- createConnection(host, username, password, requireVerification) - Method in class net.maizegenetics.pangenome.io.SFTPConnection
-
Function to create a SSH client connection and setup the lateinit variable.
- createConsensus() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Function to run createConsensus. If the user does not specify an inputConsensusHaplotypeMethod, we try to auto generate one.
- CreateContigFastaFromAssemblyGenomePlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
The sequence for each chromosome in the genome fasta file will be split based on N's. Read until an N is encountered, write the sequence as its own contig in the contig fastq output file. Skip past the "N's", start the next contig. This algorithm is subject to change during pipeline testing. Each sequence idline will be >assemblyChrom:assemblyStart:assemblyEnd INPUT: 1. The assembly genome file to process OUTPUT: 1. The newly created fasta file of contigs.
- CreateContigFastaFromAssemblyGenomePlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
- CreateContigFastaFromAssemblyGenomePlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
- CreateContigFastaFromAssemblyGenomePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
- CreateCSV_TrimmedAnchorLoading - Class in net.maizegenetics.pangenome.db_loading
-
This method takes as input 2 csv files It takes the data from FindTrimmedAnchorCoordinates.jar, then calculates new coordinates using the old ref coordinates CSV file used for loading. The data is written to another csv file that will contain: chr,trimmedStart,trimmedEnd,GeneStart,GeneEnd The genes come from the old ref coordinates CSV file. Here are the caluclations for this method: Origial anchor 2: start/end: 50358-56716 = len 6358 Regex: start/end: 387-5359 = len 4972 New anchor 2: start = oldStart + regexStart = 50358+387 = 50745 end = start + regexLen -1 = 50745 + 4972 -1 = 55716 number trimmed at start = 387 number trimmed at end = oldEnd - newEnd = 56716-55716 = 1000 Output: Method creates the csv file needed for loading ref anchors to new trimmed DB.
- CreateDBLoadScripts - Class in net.maizegenetics.pangenome.fastaExtraction
-
Simple Main program to create the script used to load all of the haplotype_caller fastas into the db TODO Refractor the logic and move execution to a plugin Created by zrm22 on 5/12/17.
- createDistanceMatrix(ntaxa, chr, currentRefRange, taxaWithInfo, taxonToVariantInfoMap) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
Function to create a disntance matrix given a set of variants for a single reference range. This will ignore Ns and indels Distance is #SNPs/(#SNPs + #RefPos)
- createEdges(haplotypeNodes) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Generates Edges based on HaplotypeNodes. Database information not used.
- createEdges(rangeToNode) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
- createEdges(leftNodes, rightNodes) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
- CreateFastaDBFiles - Class in net.maizegenetics.pangenome.fastaExtraction
-
Simple one off command line tool to create the necessary files to upload fastas to the db. TODO create these files when you extract FASTA from GVCF. No need for this step. Created by zrm22 on 5/11/17.
- createFiles(taxaListFile, outputFolder) - Method in class net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
-
- createFindProteomeFile() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- createFirstAndLastBedIntergenic(bedRanges, idMap) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Simple function to create a first and last entry for the intergenic regions before the first gene region and the last genic region.
- createFlankingList(geneRange, numFlanking, myRefSequence) - Static method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- createGATKGVCFHeader(taxaNames) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
- CreateGeneIntervalsFromConservedGFFPlugin - Class in net.maizegenetics.pangenome.db_loading
-
Creates bed file with chromosome and coordinates to be used to create PHG reference ranges. Gene names are included with each reference range. The gene name column is ignored when loading the bed file - it is there for when we want to associate reference ranges with the genes on which they were based.
- CreateGeneIntervalsFromConservedGFFPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
- CreateGeneIntervalsFromConservedGFFPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
- CreateGeneIntervalsFromConservedGFFPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
- createGenericHeader(taxaNames) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
- createGenericHeaderLineSet() - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
- createGenicRegions(idMap, gffFile, minCovCount, windowSize, secondaryIdMap, secondaryIdMapMinCovCount, maximumSearchWindow, geneRangesOutput) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
This function will create Genic regions based on the input GFF file.
- createGenotypeTableFromGVCFs(refRange, taxonToVariantListMap, referenceSequence) - Static method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
-
Deprecated.
This method takes all the VariantContexts for all of the Taxon we need in our new GenotypeTable and will create a correctly encoded GenotypeTable
- createGenotypeTableFromHaplotypeNodes(refRange, nodesWithVariantContexts, referenceSequence) - Static method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
-
Deprecated.
Method to make a genotypeTable from a list of Haplotype Nodes. This method will simply make the GenotypeTable encoding indels as either + or - depending on what is actually stored in the HaplotypeNode In other steps, the indels will be filtered out and then will be added back in when consensus is made.
- createGffChromosomeEntry(prevChrom, offset) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Create the "chromosome" type line in the gff file
- CreateGraphUtils - Class in net.maizegenetics.pangenome.api
-
- createGtvalueMap() - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
- createGVCFBlockHeaderLine(start, exclusiveEnd) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
- createGVCFFromMAF(gvcfKeyFile) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
function to create GVCF Files from anchorwave MAF files.
- createGVCFKeyFile(mafKeyFile, mafPath, gvcfServerPath) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
This function creates 2 key files based on maf key file values.
The keyfile for MAFTOGVCF is based on the exisintg MAF KeyFile values, but
with a few additional columns lacking from the WGS gvcf keyfiles, namely:
mafFile, assemblyServerPath and assemblyLocalPath.
The assemblyServerPath and assemblyLocalPath data is used when populating the genome_file_data
table in the db. The mafFile is used when determining the gvcf file name.
- CreateHapIdMapsPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Plugin to create the Haplotype Id Maps needed by the read mapping steps of the PHG.
This is very useful when running on a SLURM based system where you are unable to make SQL calls over the network.
By dumping the graph to a single JSON file read mapping can be run without needing the DB connection.
- CreateHapIdMapsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
Plugin to create the Haplotype Id Maps needed by the read mapping steps of the PHG.
This is very useful when running on a SLURM based system where you are unable to make SQL calls over the network.
By dumping the graph to a single JSON file read mapping can be run without needing the DB connection.
- CreateHapIdMapsPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
Plugin to create the Haplotype Id Maps needed by the read mapping steps of the PHG.
This is very useful when running on a SLURM based system where you are unable to make SQL calls over the network.
By dumping the graph to a single JSON file read mapping can be run without needing the DB connection.
- CreateHapIdMapsPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- createHapIdToFileNameMapping(graph, pangenomeDir) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
- createHaplotypeNodeList(fastaFile, intervalFile) - Static method in class net.maizegenetics.pangenome.api.CreateHaplotypeNodeListFromFasta
-
- createHaplotypeNodeListFromDirectory(fastaDir, intervalFile) - Static method in class net.maizegenetics.pangenome.api.CreateHaplotypeNodeListFromFasta
-
- CreateHaplotypeNodeListFromFasta - Class in net.maizegenetics.pangenome.api
-
Simple class to create a haplotype node list from a set of or a single fasta file Created by zrm22 on 8/14/17.
- createHaplotypeNodes(database, referenceRangeMap, taxaListMap, methods, includeSequences, includeVariantContext, includeHapids, localGVCFFolder, chromosomes, taxaToKeep) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
- createHaplotypeNodes(database, methods, includeSequences, includeVariantContext, includeHapids, localGVCFFolder, chromosomes, taxaToKeep) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
- createHaplotypeNodesWithVariants(database, includeHapNodes) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Creates lists of HaplotypeNodes with variant contexts corresponding to the specified nodes organized by reference Range. LCJ June 16, 2022- this function is only called from MergeGVCFPlugin:extractNodesWithVariants() MergeGVCFPlugin has been deprecated, so I am not making changes here to pull gvcf files for the variants. If this function is called at some point from a non-deprecated method, we can re-look at what changes are needed.
- createHaplotypeNodesWithVariants(database, graph) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Creates HaplotypeGraph with variant contexts corresponding to the given HaplotypeGraph.
- CreateHaplotypesFromFasta - Class in net.maizegenetics.pangenome.hapcollapse
-
Created by edbuckler on 6/19/17.
- CreateHashForFiles - Class in net.maizegenetics.pangenome.Utils
-
This class creates the MD4 or SHA-1 hash for a specified file. input: 1. Path to file for which the hash should be created. 2. digest Type: either MD5 or SHA-1 output: 1. The hash value as hex created by the digest.
- createInbredFiles(taxaListFile, outputFolder) - Method in class net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
-
- createInitialAlleles(maxKmerLen) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
This method creates a list of allele strings based on the allele set of A,C,G,T,N The size of the set will be 5 + 5^2 + 5^3 + ... + 5^n where "n" is maxKmerLen passed in and "5^n" is 5 to the nth power. For example: if maxKmerLen = 3, size of initial Allele list is: 5 + 25 + 125 = 155; if maxKmerLen = 5, size of initial Allele list is: 5 + 25 + 125 + 625 + 3125 = 3905
- createIntergenicRegions(genicRegions, maximumIntergenicGapSize, idMap, minCovCount, windowSize, secondaryIdMap, secondaryIdMapMinCovCount, maximumSearchWindow) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function to create the Intergenic regions.
For each one, we attempt to split up large regions based on the maximumIntergenicGapSize
We start from the middle of the Intergenic regions and walk out using the windowed coverage check
- createInterRegionRanges(refRanges, refSequence) - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
- CreateIntervalBedFilesPlugin - Class in net.maizegenetics.pangenome.db_loading
-
Created by zrm22 on 1/16/18. Simple Plugin to Create The interval BED files from the database. If the user provides a extendedBedFile name, it will add the windowSize to both ends of the genome interval.
- CreateIntervalBedFilesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
-
- CreateIntervalsFile - Class in net.maizegenetics.pangenome.db_loading
-
This method must be re-worked - getHaplotypeAnchorCoordinates no longer accesses the correct tables. THis method pulls ref chrom, start and end positions for ref anchors. It creates a file that is in the form needed for haplotype caller, ie 8:12921-13181
- CreateIntervalsFileFromGffPlugin - Class in net.maizegenetics.pangenome.db_loading
-
This class creates the interval files needed for running GATK haplotype caller, and the csv files needed for loading reference sequence into the database. Two sets of files are created: one set has coordinates based just on the ref gene coordinates. The other is gene coordinates plus user-specified flanking regions Algorithm: 1. read gff file, grab gene coordinates 2. For each Chromosome: merge genes that overlap, toss genes that are embedded within another gene Store list as mergedGeneList. 3. Using the mergedGeneList in 3, create 2nd per-chrom coordinate lists that includes flanking regions 4. Write files: interval format (chrom:start-end): a. mergedGeneList; b. mergedGEneList with flanking csv format (chr,anchorstart,anchorend,geneStart,geneEnd,geneName) a. mergedGeneList; b. mergedGEneList with flanking debug files: List of merged, list of embedded files written for informational purposes NOTE: the csv files contain the name of all genes contained in an anchor. This data is not stored in the DB. IT is included because the biologists have at times asked for it and this is a good place for it to be stored and retrieved. INPUT: 1. refFile: String: path to reference genome. needed to find size of chromosomes for adding flanking regions to last chrom entry. 2. geneFile: String: path to single file containing all chrom gene data in GFF format; or path to directory containing per-chrom files with gene data in GFF format. These data files must consist of GFF gene data alone, not the full gff. 3. outputBase: String: directory, including trailing "/", where output files will be written. 4. numFlanking: int: number of flanking bps to add on each end of the anchors. OUTPUT: 1. intervals file based on gene coordinates. 2. intervals file based on gene coordinates + numflanking bps 3. csv file based on gene coordinates 4. csv file based on gene coordinates + numflanking bps
- CreateIntervalsFileFromGffPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- CreateIntervalsFileFromGffPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- CreateIntervalsFileFromGffPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- createLoadScript(listOfFastaFileName, outputFileName, pathToDB, pathToLoadParamFiles, loadingExportPath, tempDBBackupDirectory) - Method in class net.maizegenetics.pangenome.fastaExtraction.CreateDBLoadScripts
-
Method which will create the loading script based on the input files. Allows for creation on cbsu with a couple file lists.
- createMAFfromAnchorwave() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
function to align the assemblies using the anchorwave proali program
This method requires the following parameters be defined in the config file
(with appropriate values for the user data):
AssemblyMAFFromAnchorWavePlugin.outputDir=
AssemblyMAFFromAnchorWavePlugin.keyFile=
AssemblyMAFFromAnchorWavePlugin.gffFile=
AssemblyMAFFromAnchorWavePlugin.refFasta=
AssemblyMAFFromAnchorWavePlugin.threadsPerRun= (optional)
AssemblyMAFFromAnchorWavePlugin.numRuns= (optional)
- createNew() - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
True indicates a new DB of this name should be created, deleting any existing DB of this name. False means return connection to existing DB or NULL
- createNew(value) - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
Set Create New DB. True indicates a new DB of this name should be created, deleting any existing DB of this name. False means return connection to existing DB or NULL
- createPairedEndReads(sequence, depth, readLength, insertSize, hapid) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
- createPathNodesForGameteGrp(taxon, conn, gamete_grp_id) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
This method connects to a database, finds the haplotypes for a specific gamete group, and creates an ordered-by-ref-range list of haplotype ids. The intended use is for path creation for Assembly and WGS input.
- CreatePHGPostgresDockerPlugin - Class in net.maizegenetics.pangenome.db_loading
-
Deprecated.
- CreatePHGPostgresDockerPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
-
Deprecated.
- CreatePHGPostgresDockerPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
-
Deprecated.
- CreatePHGPostgresDockerPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
-
Deprecated.
- createRangesWithIDFromBedFile(focusRanges) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
- createReadersForGVCFfiles(database, localGVCFFolder) - Static method in class net.maizegenetics.pangenome.api.VariantUtils
-
This function takes a database connection and a local path that holds gvcf files. It queries the db for GVCF file data from the genome_file_data table. Then converts the paths to local paths Then opens a VCFFileReader for each gvcf file. It returns a map of , to be used by all nodes in the graph
- CreateRefRangesPlugin - Class in net.maizegenetics.pangenome.pipeline
-
- CreateRefRangesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
- CreateRefRangesPlugin() - Constructor for class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
- CreateRefRangesPluginKt - Class in net.maizegenetics.pangenome.pipeline
-
- CreateRefRangeUtils - Class in net.maizegenetics.pangenome.pipeline
-
- CreateRefRangeUtils.RegionHaplotypeCount - Class in net.maizegenetics.pangenome.pipeline
-
- CreateRefRangeUtils.RegionInputData - Class in net.maizegenetics.pangenome.pipeline
-
- createRefRangeVC(refSequence, assemblyTaxon, refRangeStart, refRangeEnd, asmStart, asmEnd) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Helper method to create a Reference Range VariantContext for assemblies. The DP value is defaulted to 0 for assemblies. If this is not set, -1 is used as default in GenotypeBuilder. That causes assembly problems down the line when storing the value as a byte in a long.
- createSingleReads(sequence, depth, readLength, hapid) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
- createSingleRefRange(wrappedRefRange) - Static method in class net.maizegenetics.pangenome.hapCalling.GraphIdMapsKt
-
Unwrapper function for a single Reference Range.
- CreateSmallGenomesPlugin - Class in net.maizegenetics.pangenome.smallseq
-
This class provides a standalone plugin to create the small sequence test genome files. Files are stored as per relative paths defined in SmallSeqPaths.java This plugin also creates reference index files as may be neede by BWA, GATK or other methods. Currently there are no required parameters - each parameter has a default. NOTE: This plugin creates the indices needed, so if the user is not running through RUnSmallSeqTestsDocker, the path to samtools, bwa and picard must be given. If running from a CBSU machine, these are: /programs/bin/bwa/bwa /programs/bin/picard-tools/picard /programs/bin/samtools/samtools To run this plugin on a cbsu machine using default parameters except for the indexes tools, do this (replace your own
- CreateSmallGenomesPlugin() - Constructor for class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
- CreateSmallGenomesPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
- CreateSmallGenomesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
- createSNPVC(assemblyTaxon, startPosition, endPosition, calls, asmStart, asmEnd) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Helper method to create a SNP Variant context for assemblies. The DP value is defaulted to 0 for assemblies. If this is not set, -1 is used as default in GenotypeBuilder. That causes assembly problems down the line when storing the value as a byte in a long.
- CreateStreamGraph - Class in net.maizegenetics.pangenome.gui
-
- createTaxaListFromFileOrString(taxa) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
- CreateTestGenomes - Class in net.maizegenetics.pangenome.smallseq
-
- CreateTestGraphKt - Class in net.maizegenetics.pangenome.api
-
- createTreeMapFromFeaturesCenter(features) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
This method creates a mapping of the feature center position (posSTart + posEnd)/2 to
list of Gff3Features
- createTrimmedFastaGenotypeTable(fastaFileName, refTaxaName, idThreshold, coverageThreshold, leftTrimStart, rightTrimStart, consecFailingThresholds, consecPassingThresholds) - Static method in class net.maizegenetics.pangenome.trimAnchors.TrimGenotypeTableAnchors
-
Method which will create a trimmed GenotypeTable based on the gene start and end positions
- createTrimmedFastaGenotypeTable(fastaFileName, refTaxaName, chr, startPos, idThreshold, coverageThreshold, leftTrimStart, rightTrimStart, consecFailingThresholds, consecPassingThresholds) - Static method in class net.maizegenetics.pangenome.trimAnchors.TrimGenotypeTableAnchors
-
Method which will create a trimmed GenotypeTable based on the gene start and end positions
- CreateValidIntervalsFilePlugin - Class in net.maizegenetics.pangenome.db_loading
-
This class takes an intervals file, a genome fastas and creates a valid PHG intervals
file that can be loaded via the LoadAllIntervalsTOPHGdbPlugin.
- CreateValidIntervalsFilePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
This class takes an intervals file, a genome fastas and creates a valid PHG intervals
file that can be loaded via the LoadAllIntervalsTOPHGdbPlugin.
- CreateValidIntervalsFilePlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
This class takes an intervals file, a genome fastas and creates a valid PHG intervals
file that can be loaded via the LoadAllIntervalsTOPHGdbPlugin.
- CreateValidIntervalsFilePluginKt - Class in net.maizegenetics.pangenome.db_loading
-
- createVariantContextsFromInfo(sampleName, variantInfos) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- createVariantContextsFromMAF(refGenomeSequence) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- createVarIDtoRefAltData(taxonToPosDataMap) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
Returns a map of variantID to RefAltData for each variantId/data lookup. variantID of -1 (ref) is handled in calling method.
- createVCasRefBlock(refSequence, assemblyName, anchors, refMappings) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Method to build list of VariantContexts as RefRangeVCs - used when the reference and assembly have identical chromosome data
- createVinfoObject(vinfo) - Static method in class net.maizegenetics.pangenome.pipelineTests.GenerateRForPHG
-
- createWGSHaplotypes() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Function to create WGS based Haplotypes.
- fasta() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
Fasta File to split by chromosome
- fasta(value) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
Set Fasta File . Fasta File to split by chromosome
- fastaAlternatives - Static variable in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
-
- FastaIO - Class in net.maizegenetics.pangenome.io
-
- fastaName() - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
The name and path to which the fasta file well be written
- fastaName(value) - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
Set Fasta Name. The name and path to which the fasta
file well be written
- fastaSuffix - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- FastqcolToFastaConverter - Class in net.maizegenetics.pangenome.hapCalling
-
- FastqcolToFastaConverter(inDir, outDir, nthreads, inExt, outExt, removeAdapter, expandReads) - Constructor for class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
- FastqcolToFastaPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
This converts files in FASTQCOL format to FASTA format.
FASTQCOL files contain short-read sequencing data (primarily, as far as I can tell, generated by DArTseq)
Like FASTQ, it contains nuceotide sequence data with associated quality scores.
However, unlike FASTQ, identical reads have been collapsed into a single line in the file, and quality scores
have been averaged across all reads.
- FastqcolToFastaPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
This converts files in FASTQCOL format to FASTA format.
FASTQCOL files contain short-read sequencing data (primarily, as far as I can tell, generated by DArTseq)
Like FASTQ, it contains nuceotide sequence data with associated quality scores.
However, unlike FASTQ, identical reads have been collapsed into a single line in the file, and quality scores
have been averaged across all reads.
- FastqcolToFastaPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
This converts files in FASTQCOL format to FASTA format.
FASTQCOL files contain short-read sequencing data (primarily, as far as I can tell, generated by DArTseq)
Like FASTQ, it contains nuceotide sequence data with associated quality scores.
However, unlike FASTQ, identical reads have been collapsed into a single line in the file, and quality scores
have been averaged across all reads.
- FastqcolToFastaPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- fastqDir() - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Name of the Fastq dir to process.
- fastqDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Set Fastq dir to process. Name of the Fastq dir to
process.
- fastqDir() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Name of the Fastq dir to process.
- fastqDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Fastq dir to process. Name of the Fastq dir to
process.
- fastqDir() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Name of the Fastq dir to process.
- fastqDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set Fastq dir to process. Name of the Fastq dir to
process.
- fastqDir() - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
the directory to which the simulated read fastq will
be written. The default will write to a temp directory,
which will not be available after the plugin finishes.
- fastqDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
Set Fastq Dir. the directory to which the simulated
read fastq will be written. The default will write
to a temp directory, which will not be available after
the plugin finishes.
- fastqDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- fastqDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- FastqDirToMappingPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Deprecated.
- FastqDirToMappingPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Plugin to Take a Directory of Fastq files and will map them to the pangenome using FastqToMapping Plugin.
- FastqDirToMappingPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- fastqGroupingFile() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Grouping file created by MergeFastqPlugin
- fastqGroupingFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Fastq Grouping File. Grouping file created by MergeFastqPlugin
- fastqName() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
The name of the fastq file used to create the path. This must be the name only, not the full path. Not required if the path and count data can be retrieved using other parameters.
- fastqName(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Set Fastq name. The name of the fastq file used to create the path. This must be the name only, not the full path. Not required if the path and count data can be retrieved using other parameters.
- FastqToHapCountMinimapPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Deprecated.
- FastqToHapCountMinimapPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
This class will be the 3rd attempt for a genotyping pipeline.
- FastqToHapCountMinimapPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- FastqToKmerCountPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Deprecated.
- FastqToKmerCountPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
-
Deprecated.
- FastqToMappingPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Plugin to map reads to the pangenome using Minimap2
- FastqToMappingPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Plugin to map reads to the pangenome using Minimap2
- FastqToMappingPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- fileName() - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
Name from the SAM or Fastq file to know which key file
record to output. This will look at the filename column
- fileName(value) - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
Set File Name. Name from the SAM or Fastq file to know
which key file record to output. This will look at
the filename column
- fillGaps() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
When true, if the maf file does not fully cover the
reference genome any gaps in coverage will be filled
in with reference blocks. This is necessary if the
resulting GVCFs are to be combined.
- fillGaps(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Set Fill Gaps. When true, if the maf file does not
fully cover the reference genome any gaps in coverage
will be filled in with reference blocks. This is necessary
if the resulting GVCFs are to be combined.
- FillIndelsIntoConsensus - Class in net.maizegenetics.pangenome.hapcollapse
-
This class is created to fill in the agreeing indels removed from the consensus haplotypes during the merge process. There are various merge rules for when the indels disagree.
- FillIndelsIntoConsensus.INDEL_MERGE_RULE - Enum in net.maizegenetics.pangenome.hapcollapse
-
- filter(graph) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
- filterAndExtractFasta(gvcfFile, outputDirectory, refSeq, intervalFile, filterProperties, isAssembly, bcfToolsPath) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter
-
Method to filter the gvcf and extract the fasta using the config file.
- filterAndExtractFasta(gvcfFile, outputDirectory, refSeq, intervalFile, poissonProbabliltyBounds, isAssembly, bcfToolsPath) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter
-
Old method using a poissonProbability tuple to filter based on depth. This should be deprecated once we tune the pipeline TODO deprecate this method once the pipeline is tuned.
- filterBadAlignments(genotypeTable, maxDist, minSiteCount, minMAF) - Static method in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
-
This method eliminates high distances alignments after all GAPs have been converted to N, and then it filters on coverage and minimum MAF
- FilterBAMAndGetStatsPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Plugin to Filter out the BAMs and build a stats file to get numbers of each of the CIGAR operators for each reference range as well as how many reads hit each one.
- FilterBAMAndGetStatsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Plugin to Filter out the BAMs and build a stats file to get numbers of each of the CIGAR operators for each reference range as well as how many reads hit each one.
- FilterBAMAndGetStatsPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Plugin to Filter out the BAMs and build a stats file to get numbers of each of the CIGAR operators for each reference range as well as how many reads hit each one.
- FilterBAMAndGetStatsPlugin.RefRangeStats - Class in net.maizegenetics.pangenome.hapCalling
-
- FilterBAMAndGetStatsPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- filterCoordsOverlaps(coordsNoEmbedded, snpFile, coordsFinal) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Takes a mummer coords file and searches for overlaps. All of the overlap goes to the first entry. If splitting in this manner results in a split in the middle or an assembly deletion, then split is adjusted so the deletion is contained in the first entry of the overlapped pair. The snpFile is used to determine indel positions. For now, assembly insertions may be split. This has not been a problem for variant context processing.
- filteredGraph() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- filteredGraph() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
Filters myGraph using readHapids based on maxNodesPerRange, minReadsPerRange,
removeRangesWithEqualCounts, and maxReadsPerKB
- FilterFastqUsingBAMPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Created by zrm22 on 9/13/17.
- FilterFastqUsingBAMPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
- FilterGraphPlugin - Class in net.maizegenetics.pangenome.api
-
- FilterGraphPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
- filterGVCF(inputFile, outputFile, configProperties, isAssembly, bcftools) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter
-
- FilterGVCFPlugin - Class in net.maizegenetics.pangenome.gvcfFiltering
-
- FilterGVCFPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
- FilterGVCFSingleFilePlugin - Class in net.maizegenetics.pangenome.gvcfFiltering
-
This plugin is called from groovy script CreateHaplotypesFromBAM.groovy The gvcf remote file information will be uploaded to the db:genome_file_data table when LoadHaplotypesFromGVCFPlugin is run. So here we only need the docker/singularity specific path for storing the data. If the user is to sftp the files, then isGvcfLocal will be false, and the gvcfRemoteServer parameter will be a real server address and a path.
- FilterGVCFSingleFilePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
- filterHaplotypeGraph(graph) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
This method filters a HaplotypeGraph and sets the myGraph field of the class to the result. The resulting filtered HaplotypeGraph will be used for any subsequent method calls.
- filterHaplotypeGraph(graph, rangesToKeep) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
This method filters a HaplotypeGraph and sets the myGraph field of the class to the result. The resulting filtered HaplotypeGraph will be used for any subsequent method calls.
- filterOnTaxa(graph) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- filterRead(currentSamRecord, pairedEnd, clippingFilter) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
- filterRefRanges() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
Name of ref range filter file
- filterRefRanges(value) - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
Set Filter Ref Range File. Name of ref range filter file
- finalSnpFiltering(outputSNPS, deltaFilePrefix, chrom) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
- findAlignmentsToRemove_fromMinus1Filter(origList) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Traverse a list of mummer coords entries. Create lists of alignments that have a minimum of 3 in a row where assembly is in the same direction (forward or reverse) and the distance between the end of one entry and the beginning of the next is > 0.01 percent. Return a concatenated list of all the entries kept from the original file. This method is expected to be used with a mummer coords file created from a delta file filtered with the -1 option.
- findAlignmentsToReturnFromAfterMinusGFilter(removedList, gList) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Takes a list of mummer4 coordinates removed during delta-filter with -g and determines which coordinates should be returned. Those returned have reference range coordinates that fall between 2 existing kept alignment reference range coordinates, and whose assembly coordinates fall between the assembly coordinates of the 2 ranges. Most often, these will be alignments where the assembly aligned on the reverse strand. Nothing is added back that falls before the start of the coordinates created with delta-filter -g, or after the end of the delta-filter -g list of coordinates. If a removed entry falls before the first of the pair of gList entries, and extends into the second gList entry, it is not added. The entries returned are limited to alignments where the ref length is at least 1000 bps. Any entries added that overlap each other will be handled in later processing when all overlaps are handled. The mummer4 delta-filter with -g performed 1-1 global alignment with no rearrangements. This purpose of findAlignmentsToReturn() is to return inversions that appear on the diagonal. NOTE: This method is obsolete, but kept to facilitate user desire to process with mummer -G filtering
- findAlleleIDFromDB(allele, dbConn) - Static method in class net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
-
From an allele string, compute the hash value and search for a corresponding ID in the DB alleles table.
- findAsmIndelStart(snpEntries) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
- findAsmUpdatesForGVCF(gvcfFile, refIdToRefRangeDataMap) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
- findBestDiploidPath() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- FindBestDiploidPathKt - Class in net.maizegenetics.pangenome.hapCalling
-
- findBestPath() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- findBestRefRange(refRangeToIdMapping, maxRefRangeError) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to check to see if the read hits a multiple reference ranges less than maxRefRangeError
Basically this is to filter out any reads which hit multiple reference ranges equally well
- findBestRefRangeFromRecords(refRangeToIdMapping, maxRefRangeError) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Function to check to see if the read hits a multiple reference ranges less than maxRefRangeError
Basically this is to filter out any reads which hit multiple reference ranges equally well
- findEndPosition(idMap, seqname, lastPostion, strand, minCovCount, windowSize, secondaryIdMap, secondaryIdMapMinCovCount, maximumSearchWindow) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function to find the End position starting from a start point.
This will walk out based on the strand until it hits a windowed region which passes the coverage check.
- findFlankingEndPos(geneRange, data, numFlanking, chromLen) - Static method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- findFlankingStartPos(geneRange, data, numFlanking, chromLen) - Static method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- findGaps(target, source) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MafUtils
-
Method takes 2 lists of Maf Records, returns the gaps indicating which
positions appear in the source that are not in the target. The calling
method then augments the target with sequence from the gaps indicated
by the findGaps method.
- findHapClusterHighCoverage(baseAlign, minSites, maxDistance) - Static method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Clusters taxa using high coverage samples as the nucleation points.
- FindHaplotypeClustersPlugin - Class in net.maizegenetics.pangenome.hapcollapse
-
Deprecated.
- FindHaplotypeClustersPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
- FindHaplotypeClustersPlugin.CLUSTER_METHOD - Enum in net.maizegenetics.pangenome.hapcollapse
-
Deprecated.
- findMostLikelyParents(refRangeToHapIdSetCounts, maxParents, minCoverage) - Method in class net.maizegenetics.pangenome.hapCalling.MostLikelyParents
-
Finds the most likely parents for a set of hapid counts from read mappings.
- findNonOverlappingGlistPair(gList, glistIdx) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Given a list of mummer coords entries and an index, finds the entry where this entry and the one before it have no overlaps in either the ref or assembly coordinates. The index returned is for the second of the 2 entries. This method is used when searching for mummer delta file entries removed during -g delta filtering that we would like to return.
- findPathsFromDBReadMappings(graph, keyFile) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Method that gets a list of read mappings from the database for a specific method and writes a path to the database
for each read mapping record
- findPathsFromDBReadMappingsMultithread(graph, keyFile) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Method to find paths by extracting the read mappings from the DB.
Then it will aggregate the counts together by summing the counts for a given hapId set.
- FindProteomeGenesInAssembly - Class in net.maizegenetics.pangenome.pipelineTests
-
NOTE: Needs to be re-worked with new db. The PHG calls are obsolete, need calls for new schema. Input: 1. the db from which to pull the assembly/haplotype data 2. the reference genome for pulling the gene sequence (a subset of the anchor sequence) 3. the name of the reference line as stored in the db (e.g. B73Ref) 4. the name of the assembly as stored in the db, e.g. (W22Assembly) 5. name of the line from haplotypeCaller as stored in the db (e.g. W22_Haplotype_Caller) or NONE if this line was not processed via haplotype caller. 6. Tab-delimited file containing list of anchorids, the gene start/end on which the anchor is based, and whether the gene is a proteome gene. 7. The output directory for writing files. Output: 1. A tab-delimited file containing the headers: AnchorID\tChromosome\tGene\tGeneInProteome\tAssemblyHasAnchor\tGeneSeqIn_\tGeneSeqIn_\tGeneSeqInBoth\tGeneSeqInNeither 2. Console output that may be re-directed to a file. THis output contains counts and calculated percentages. Algorithm: - read reference genome into GenomeSequence object - get assembly and haplotype caller anchor infor from db - read geneFile, for each entry: - note if is proteome - if anchor is present in assembly, mark counts for proteome/non-proteome, and check if gene sequence is part of this line's anchor sequence for this id - if anchor is present in haplotype_caller, mark counts for proteom/non-proteome, and check if gene sequence is part of this line's anchor sequence for this id. - close files, - calculate percentages
- FindRampSeqContigsInAssemblies - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This method takes a fasta of ramp seq short sequences, and looks for them in an assembly genome. This is for Dan. Looking for exact matches of the 9000 across all entries in the fasta file. Look for both orig sequence, and reverse complement of sequence. This one works well - it runs each assembly in sequence. When processing the assemblies, it parallelizes over every rampSeq contig in the rampSeq map (file read into map). This speeds things up considerably from parallel processing just over the assemblies. Using indexOf(seq,startPos) still seems quicker than knuth-morris-pratt method, perhaps because of overhead of the latter. INPUT: - fasta of rampSeq short contigs - directory path, including trailing / where assembly genome fasta files live - directory path, including trailing / to which output files will be written OUTPUT: - tab-delimited files without headers, but the columns are BED file positions (0-based, inclusive/exclusive). ContigName AssemblyIDLine startPos endPos Strand In the above, Strand is whether the forward (as presented in file) or reverse-compliment of the strand matched in the assembly file. THe start/end positions are 0-based, inclusive/exclusive as for bedfiles. There is 1 tab-delimited file generated for each assembly. The file name reflects the assembly name.
- findRefIndelStart(refSnpPos, snpEntries) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Find the lowest reference start entry from a mummer snp file list of entries. There could be more than 1 string of indels for this asm snp. Find the start and end of the string of indels whose positions overlap the reference position for the SNP in question. Return the start position and the length of this string of indels
- findTaxonRefCoverage(startPos, maxRefLen, tList, taxonToPosDataMap, maxError, minTaxaCoverage) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
- FindTrimmedAnchorCoordinates - Class in net.maizegenetics.pangenome.db_loading
-
NOTE: This version works on the REF only. The assemblies do not have their coordinates in the fasta files - they only have the start, not the end. OH - but I could get it from the length. Due to time, I'm not going to mess this one up. I"ll write another one for assemblies and merge them later. Method takes - a refAnchor fasta file, (I dumped reference anchors from the pre-trimmed db) - a list of files from a directory that contain the trimmed versions on a per-anchor basis. Find the start and end of the trimmed sequence in the ref sequence. The start is where it matches. The end is the length of the trimmed sequence added to the start. Output: The important output is the csv file that will be used to load the new reference anchors to the "trimmed" database.
- FindTrimmedAssemblyCoordinates - Class in net.maizegenetics.pangenome.db_loading
-
THis file is similar to FindTrimmedAnchorCoordinates used for the reference. The difference is the ref has all anchors. Assemblies do not. We need to read the assembly fasta, determine which anchor is represented The anchor is there in the idLine - the last value after the space, e.g. >1:44289:49837;chr1:1 1 THis is creating a fasta, but it isn't useful because the IDline is not what is needed when loading into the DB. Idline must have >B73RefChrom:B73startpos:B73EndPos;assemblyChrom:assemblyStart:asemblyEnd anchorid
- findUserPHGVersion(versionList) - Static method in class net.maizegenetics.pangenome.pipeline.PipelineUtilsKt
-
This function finds the lowest PHG version from a list of PHG versions.
The return value should be of the format X.X.X
- findVCListForAnchor(positionRangeToVariantContextMap, refStart, refEnd) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
- firstReferenceRange() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns the first reference range in this graph.
- firstReferenceRange(chr) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns the first reference range for the given chromosome.
- forceDBUpdate() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Parameter to force the DB to update. If this is set
to true and the DB is incompatible with the current
PHG code, this will automatically update the DB if
it can.
- forceDBUpdate(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Force D B Update. Parameter to force the DB to
update. If this is set to true and the DB is incompatible
with the current PHG code, this will automatically
update the DB if it can.
- forceDBUpdate() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Parameter to force the DB to update. If this is set
to true and the DB is incompatible with the current
PHG code, this will automatically update the DB if
it can.
- forceDBUpdate(value) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Set Force D B Update. Parameter to force the DB to
update. If this is set to true and the DB is incompatible
with the current PHG code, this will automatically
update the DB if it can.
- forEachRemaining(action) - Method in class net.maizegenetics.pangenome.api.GraphSpliterator
-
- formatMethodParamsToJSON(parameterList) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
This method takes a Map of parameterName to parameterValue, and formats them into a JSON string. This string will be used by the calling method as the description entry for the PHG methods table.
- fParameter() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
The f parameter used by minimap2. If the sr preset
(-x sr) is used then this parameter takes the form
f. From the minimap2 man page: If integer,
ignore minimizers occuring more than INT1 times. INT2
is only effective in the --sr or -xsr mode, which sets
the threshold for a second round of seeding.
- fParameter(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set F Parameter. The f parameter used by minimap2.
If the sr preset (-x sr) is used then this parameter
takes the form f. From the minimap2 man
page: If integer, ignore minimizers occuring more than
INT1 times. INT2 is only effective in the --sr or -xsr
mode, which sets the threshold for a second round of
seeding.
- freqChartHaplotypeCollapse(inputFile, outputDir) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- freqHaplotypeCollapse(inputFile, outputDir) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- fullRefCoordinateToChromCoordinate(coordinates) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- fullyConnected() - Method in class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
Set to true to have adjacent reference ranges fully
connected
- fullyConnected(value) - Method in class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
Set Fully Connected. Set to true to have adjacent reference
ranges fully connected
- gbsDepth() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Depth for GBS
- gbsDepth(value) - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Set GBS Depth. Depth for GBS
- geneEnd() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
-
- geneFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
Tab delimited .txt file containing gene-only GFF data from reference GFF file,
- geneFile(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
Set Gene File. Tab delimited .txt file containing gene-only GFF data from reference GFF file,
- GeneGFFData - Class in net.maizegenetics.pangenome.db_loading
-
- GeneGFFData(start, end, name) - Constructor for class net.maizegenetics.pangenome.db_loading.GeneGFFData
-
- geneLength() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Number of base pairs to include for each gene region
- geneLength(value) - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Set Length Of Genes. Number of base pairs to include for each gene region
- generatedFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
Full path with file name to write created intervals file
- generatedFile(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
Set Output File. Full path plus file name to write created
intervals file
- GenerateHaplotypeCallerScripts - Class in net.maizegenetics.pangenome
-
- GenerateRForPHG - Class in net.maizegenetics.pangenome.pipelineTests
-
This class holds methods and classes to generate R code for PHG classes. It also creates vectors that hold PHG database table information.
- geneStart() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
-
- genicRangesFile() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Optional output file name for the gene ranges created
by finding conserved breakpoints near genes from the
gff file. If no name is supplied the genic range file
will not be written.
- genicRangesFile(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Ouput Gene Ranges. Optional output file name for
the gene ranges created by finding conserved breakpoints
near genes from the gff file. If no name is supplied
the genic range file will not be written.
- genicRangesToBedFile(bedFile, bedRanges) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Simple function to output a bed file
- GenoHaploData - Class in net.maizegenetics.pangenome.db_loading
-
Object to hold data needed to populate the genotypes and haplotypes tables. These tables should be populated at the same time. The data is stored in a single object to facilitate making a single call to WGSSqlite to populate both. Hopefully combining them won't be a problem when we need to grab data later. I assume we'd want data from both tables.
- GenoHaploData(ploidy, is_ref, line_name, line_data, isPhasedAcrossGenes, isPhasedAcrossChromosomes, hapNumber, phasingConfidence) - Constructor for class net.maizegenetics.pangenome.db_loading.GenoHaploData
-
- genomeData() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Path to tab-delimited file containing genome specific
data with header line:
Genotype Hapnumber Dataline Ploidy Reference GenePhased
ChromPhased Confidence Method MethodDetails
- genomeData(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Set Genome Data File. Path to tab-delimited file containing
genome speciic data with header line:
Genotype Hapnumber Dataline Ploidy Reference GenePhased
ChromPhased Confidence Method MethodDetails
- genomeFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
Input assembly genome file from which to pull sequence
- genomeFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
Set Assembly Genome. Input assembly genome file from which to pull sequence
- genomeFileID() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
- genomeNames - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- genomeSequence(startSite, lastSite) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
- genomeSequence(startSite, lastSite) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- genomeSequenceAsString(startSite, lastSite) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
- genomeSequenceAsString(startSite, lastSite) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- genomeSize() - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- genotype(chrom, position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
- genotype(chrom, positionObject) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
- genotype(chrom, position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- genotype(chrom, positionObject) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- genotypeAsString(chrom, position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
- genotypeAsString(chrom, positionObject) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
- genotypeAsString(chrom, startSite, endSite) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
- genotypeAsString(chrom, position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- genotypeAsString(chrom, positionObject) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- genotypeAsString(chrom, startSite, endSite) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- genotypeString() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- genotypeTable(graph, range, taxon) - Static method in class net.maizegenetics.pangenome.api.GraphToGenotypeTable
-
- genotypeTable(graph, range, taxaList) - Static method in class net.maizegenetics.pangenome.api.GraphToGenotypeTable
-
- genotypingDebugDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- genotypingDebugDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- genotypingFastqDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- genotypingFastqDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- genotypingKeyFile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- genotypingKeyFileDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- genotypingPathKeyFile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- genotypingPathKeyFileDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- get(kmer) - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- get(kmerSeq) - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- getAdjustedMummerCoordEntry(entry, adjustLen, asmAscending) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
- getAlignment() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- getAllChrVCFStats(summaries) - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
- getAlleleDepths() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getAllTaxaGroupNames() - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns a list of all taxa group names from the taxa_groups table
- getAllTaxaGroupNames() - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getAltAllele() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getAltDepth() - Method in class net.maizegenetics.pangenome.hapcollapse.RefAltData
-
- getAltDepth() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- getAltPL() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- getAltRecord() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.MAFRecord
-
- getAnchorDataMapping() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- getAnchorDataMapping() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin.ChromosomeGVCFRecord
-
- getAnchorFromIntervalsFile(intervalsFile, chrom) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- getAnchorRangeSet(anchorEntries) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Create a RangeSet from a map of ranges
- getAnchorRangeSet(anchorOverlapEntries) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- getAS() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- getAS() - Method in class net.maizegenetics.pangenome.hapCalling.SecondaryStats
-
- getAsmChr() - Method in class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- getAsmChrom() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getAsmDBName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- getAsmDBName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- getAsmEnd() - Method in class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- getAsmEnd() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.UpdateData
-
- getAsmEnd() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getAsmEndPos() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- getAsmFasta() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- getAsmFasta() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- getAsmFullGenomeFasta() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- getAsmLocalPath() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- getAsmServer() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- getAsmServerPath() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- getAsmStart() - Method in class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- getAsmStart() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.UpdateData
-
- getAsmStart() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getAsmStartPos() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- getAsmStrand() - Method in class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- getAsmStrand() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.UpdateData
-
- getAsmStrand() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getBasesAligned() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- getBasesDeleted() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- getBasesGapped() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- getBasesInserted() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- getBestEditDistance() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- getButtonName() - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.api.MethodTableReportPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.api.ReadMethodTablePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.api.ReferenceRangeSummaryPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.api.WriteGraphAsGFAPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.ChangeDBMethodTypePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeleteReadMappingPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.RankingFilePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.io.PathsToFastaPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.pipeline.MakeDefaultDirectoryPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.pipeline.MakeInitialPHGDBPipelinePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
- getButtonName() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
- getChecksumForFile(file, protocol) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
- getChecksumForString(seq, protocol) - Static method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- getChr() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin.RefrangeInfo
-
- getChr() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getChrom() - Method in class net.maizegenetics.pangenome.hapcollapse.RefAltData
-
- getChrom() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- getChrom() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.RefRangeData
-
- getChromName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- getChromNamesForHaplotype(line_name, hap_number, version) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Method grabs a list of distinct chromosome names for a genome_interval version
- getChromNamesForHaplotype(line_name, hap_number, version) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getChrSize() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- getClient() - Method in class net.maizegenetics.pangenome.io.SFTPConnection
-
- getConsensusDataMap() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
-
- getCoordsEntriesForAnchor(anchorRange, coordsFileRefToDataMap) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- getCoordsRangeMap(coordsList, chrom) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Create range map from list of entries from a Mummer coordinates file
- getCount() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdSetCount
-
- getCount() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- getCount() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- getCurrentChrom() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- getCurrentChrom() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin.ChromosomeGVCFRecord
-
- getCurrentEmissionProbabilities() - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- getCurrentNode() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
- getCurrentRefRangeIndex() - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- getCurrentTaxon() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- getCurrentTaxon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin.ChromosomeGVCFRecord
-
- getDataFromAssembly(assemblyFile, outputFile) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- GetDBConnectionPlugin - Class in net.maizegenetics.pangenome.db_loading
-
Plugin takes a configFile with db specifics and a boolean indicating whether a new db shoudl be created. Output is a db COnnection object. INPUT: Config file containing these 5 lines (additional lines are ignored) host= user= password= DB= DBtype= boolean: TRUE means create a new db if it doesn't exist, false means return null if db doesn't exist If db exists and boolean is TRUE, the db will be deleted and a new one of that name created. OUTPUT: A db Connection object
- GetDBConnectionPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
- GetDBConnectionPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
- GetDBConnectionPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
- getDbTaxaNames() - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Gets a list of the taxa currently in the database. Taxa are identified by the line_name field of the genotypes table
- getDbTaxaNames() - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getDe() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- getDe() - Method in class net.maizegenetics.pangenome.hapCalling.SecondaryStats
-
- getDecodedReadMappingForMappingId(readMappingId, graph) - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingDecoder
-
- getDelLargest() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getDelLowerQuartile() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getDelMedian() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getDelUpperQuartile() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getDiploidPath() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
Finds the most likely diploid path through myGraph given readHapids.
Before the path is imputed, the graph is filtered based on maxNodesPerRange, minReadsPerRange,
removeRangesWithEqualCounts, and maxReadsPerKB then missing sequence nodes are added and, finally,
the nodes are split into individual taxa if splitNodes is true.
- getDistinctGffIds(gffSet) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Get list of distinct GFF IDs in the full Gff3Feature Set
NOTE: what this returns is based on how the GFF3 has the IDs defined.
If user wants a count of something like "Zm000a2" but the ID is:
"ID=gene:Zm000a2", it won't be what they want. Because "ID="gene:Zm000a2"
and "ID=transcript:Zm000a2" are different IDs.
- getDistinctGffIdsByChrom(gffSet) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Creates map of contig(chrom) to set of distinct Gff3Feature ids
associated with that contig
- getEditDistance() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- getEnd() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin.RefrangeInfo
-
- getEnd() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- getEnd() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- getEnd() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.RefRangeData
-
- getEndPos() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getEntryFromTabDelimitedLine(mline, entryColumn, totalColumns) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Returns the value for a specific column in a tab-delimited string
- getExpandReads() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
- getF() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbabilityWithInbreeding
-
- getFastaInfo() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.ResultChannelData
-
Deprecated.
- GetFastaSequenceLengths - Class in net.maizegenetics.pangenome
-
Created by terry on 3/19/17.
- getFileGroupName() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- getFileGroupName() - Method in class net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord
-
- getFileNameToPathMap() - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- getGameteGroupIDFromTaxaList(gametes) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Takes a list of taxa and returns the corresponding gamete_group_id or 0
- getGameteGroupIDFromTaxaList(gametes) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getGameteId() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- getGenoidFromLine(line_name) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Return genoid
- getGenoidFromLine(line_name) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getGenoidsForTaxa(taxa) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getGenomeFileHashFromGenoidandFile(genoid, file) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Given a genoid and a file name, return the hash value and id for that entry in the genome_file_data table. If there is no entry, return null
- getGenomeFileHashFromGenoidandFile(genoid, file) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getGenomeFileIdFromGenoid(genoid) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Gets the id from the genome_file_data table based on the genoid .
- getGenomeFileIdFromGenoid(genoid) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getGenomeFileIdFromGenoidAndFile(genoid, file) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Gets the id from the genome_file_data table based on the genoid and a filename
- getGenomeFileIdFromGenoidAndFile(genoid, file) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getGenomeSequenceValues() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- getGenoName() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- getGenotype() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getGFFEntriesPerChrom(gffSet) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Counts the gff entries per chromosome
- getGffFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- getGhd() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- getGVCFforDownload(gvcfIdToRemotePath) - Static method in class net.maizegenetics.pangenome.api.VariantUtils
-
GIven a Map of gvcfFileIds to remote path (data from the genome_file_data table), return a list of servers and the gvcf files do be downloaded from them. It is required that each "path" have a server indicated, even if it is local.
- getGvcfServerPath() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- getHapCountsIDAndDataForVersionMethod(method) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
This method pulls the haplotype_counts_id with corresponding genotypes line name and data for all DB entries based on the supplied method
- getHapCountsIDAndDataForVersionMethod(method) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getHapCountsIDAndPathsForMethod(method) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
THis method pulls the haplotype_counts_id and corresponding path for all entries in the paths table with the specified method.
- getHapCountsIDAndPathsForMethod(method) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getHapId() - Method in class net.maizegenetics.pangenome.api.RPHGMethodsKotlin.HaplotypeSequences
-
- getHapId() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- getHapidForGenoidHapNumber(genoid, hap_number) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns hapid for given line name and hap_number
- getHapidForGenoidHapNumber(genoid, hap_number) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getHapidHapNumberLineNamesForLines(lineNames) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Retrieves line name and hapnumber, and returns them with the hapid. hapid is the key in the map. THe line name and hap number are concatenated with an underscore and returned as the string value for each hapid.
- getHapidHapNumberLineNamesForLines(lineNames) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getHapidMapFromLinenameHapNumber() - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns a map of created from the genotypes and haplotypes table.
- getHapidMapFromLinenameHapNumber() - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getHapIdMultiset() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin.ReadMappingResult
-
- getHapIdSeq(phgObj, hapIds) - Method in class net.maizegenetics.pangenome.api.RPHGMethodsKotlin
-
Return sequence information from haplotype ID input
- getHapIdSet() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdSetCount
-
- getHapIdSet() - Method in class net.maizegenetics.pangenome.hapCalling.SingleHapMapping
-
- getHapidsForGenoid(genoid) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns list of hapids for a given line name
- getHapidsForGenoid(genoid) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getHapIdsForPos(position) - Method in class net.maizegenetics.pangenome.hapCalling.PositionToRefAndAltHaplotypes
-
- GetHapIdsForTaxonPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Class takes a configfile with database connect information, an output directory,
a set of methods, and an optional taxa list. It will create one file per taxon with a single column containing
the haplotype_ids for that taxon/gamete from the haplotypes table.
- GetHapIdsForTaxonPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
Class takes a configfile with database connect information, an output directory,
a set of methods, and an optional taxa list. It will create one file per taxon with a single column containing
the haplotype_ids for that taxon/gamete from the haplotypes table.
- getHapIdToLengthMap() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- getHapIdToRefRangeMap() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- getHapIdToSecondaryStats() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- getHapIdToSequenceLength(graph) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
- getHapIdToStatMap() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin.ReadMappingResult
-
- getHapIdToTaxaList() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- getHaplotypeIDFromFastaIDLine(idLine, methodName) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns the haplotype_id from the haplotypes table based on the gamete_grp_id (calculated from the taxa list), the ref_range_id (calculated from the ref coordinates part of the idline) and the method.
- getHaplotypeIDFromFastaIDLine(idLine, methodName) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getHaplotypeList(id) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Given a haplotype_list_id, query the haplotype_list table and return a list of haplotypes stored for that ID, or an empty list if there were none.
- getHaplotypeList(haplist_id) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getHaplotypeListId() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- getHaplotypeListIdForGraph(graph, phgAccessor) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
- getHaplotypeListIDfromHash(hash) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Given an MD5 hash value, returns the db id for that entry, or 0 if none exist
- getHaplotypeListIDfromHash(hash) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getHaplotypeMethodForHapids(hapidList) - Static method in class net.maizegenetics.pangenome.hapCalling.ReadMappingUtils
-
- getHaplotypeMethodsForReadMappings(readMap, numberOfRefRanges) - Static method in class net.maizegenetics.pangenome.hapCalling.ReadMappingUtils
-
- getHapToRefRangeMap(graph) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to create a HapId to RefRange mapping for all of the HapIds in a graph
- getHostIpAddr() - Static method in class net.maizegenetics.pangenome.smallseq.CreateTestGenomes
-
- getIcon() - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.api.MethodTableReportPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.api.ReadMethodTablePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.api.ReferenceRangeSummaryPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.api.WriteGraphAsGFAPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.ChangeDBMethodTypePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeleteReadMappingPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.RankingFilePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.io.PathsToFastaPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.pipeline.MakeDefaultDirectoryPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.pipeline.MakeInitialPHGDBPipelinePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
- getIcon() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
- getId() - Method in class net.maizegenetics.pangenome.api.Method
-
- getId() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.UpdateData
-
- getIdToRefRangeMap() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.ResultChannelData
-
Deprecated.
- getInbreedCoef() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- getInbreedCoef() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getIndelLargest() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getIndelLowerQuartile() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getIndelMedian() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getIndelRanges(coordinates) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
- getIndelSizes() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- getIndelSizeStats(indelSizes) - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
Given list of indel sizes, return number, mean length, quantiles length, and longest for indels, insertions, and deletions
- getIndelUpperQuartile() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getInExt() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
- getInsLargest() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getInsLowerQuartile() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getInsMedian() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getInstance(sequence, referenceRange, qualityScore, seqHash) - Static method in class net.maizegenetics.pangenome.api.HaplotypeSequence
-
Factory method to create HaplotypeSequence This allows a copy of the HaplotypeSequence to be returned instead of the original mutable object
- getInstance(sequence, referenceRange, qualityScore, seqHash, seqLen) - Static method in class net.maizegenetics.pangenome.api.HaplotypeSequence
-
Factory method to create HaplotypeSequence This allows a copy of the HaplotypeSequence to be returned instead of the original mutable object Haplotype sequences are always gzip compressed, stored as byte array. This signature used when creating sequence from DB's byte array
- getInstanceFromHapidCountMap(nodes, hapidCountMap, probCorrect) - Static method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
-
- getInstanceFromHapidCounts(nodes, hapidCounts, probCorrect) - Static method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
-
- getInstanceFromNodeCounts(nodes, nodeCounts, probCorrect) - Static method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
-
- getInsUpperQuartile() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getIntervalRangesWithIDForChrom(chrom) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns sorted treeRangeMap of Positions for specified chromosome
- getIntervalRangesWithIDForChrom(chrom) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getKeyFileColumnNameMap() - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- getKeyFileEntry() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingInput
-
- getKeyFileEntry() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- getKeyFileEntry() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingInput
-
- getKeyFileEntry() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- getKeyFileLines() - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- getKeyFileRecord() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin.ReadMappingResult
-
- getKeyFileRecordsToFileMap() - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- getKmerArray() - Method in class net.maizegenetics.pangenome.hapCalling.KmerToRefRangeIdToPurgeArray
-
- getKmerPrefix() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- getKmerSize() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- getLen() - Method in class net.maizegenetics.pangenome.hapcollapse.RefAltData
-
- getLengthOfMapping() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- getLikelyParents() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- getLikelyParents() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- getLikelyParents() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- getLineNameHapNumberFromHapid(hapid) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Method to retrieve both a line name and the hap number given a hapid.
- getLineNameHapNumberFromHapid(gameteid) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getLineNamesFromGameteGroup(db) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
- getListOfHapIds() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- getLocalGVCFFile() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- getLongFromRefAltData(rad) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
RefAltData comes from processing the Longs stored for each haplotype. It is used for consensus processing. Different data is available than is with the VariantMappingData used for processing single haplotypes.
- getLongFromVMData(vmID, vmd) - Static method in class net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
-
Takes an ID and a VariantMappingData object and creates a list of variant_ids with additional data.
- getLongListOfVariantData(variantMappingDataList, hashIDMap) - Static method in class net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
-
Takes a list of variantIdhash to VariantMappingData and creates a list of "long" values, that represents the variant context for each entry
- getLongRefRecord(refLen, refDepth, startPos) - Static method in class net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
-
Takes a reference length, depth and start position on the chromosome. Returns an encode long holding this information. format: 1bit=ref | 2 bytes 7 bits = refLength | 1 bytes=refDepth | 4 bytes=position on chrom
- getLongVariantRecord(vmID, refDepth, altDepth, isIndel, otherData) - Static method in class net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
-
Takes a variantMapping id, reference depth, alternate depth, indication as to if is an indel, and a dummy int Returns a long formatted with this data. format: 4 bytes= variant_mapping table id | 1 byte=refDepth | 1 byte=altDepth | 1 bytes=isIndel | 1 byte unused
- getMap() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdMultiset
-
Method to get out the backing Map. This can be more easily worked with once everything is added to the Multiset.
- getMap() - Method in class net.maizegenetics.pangenome.hapCalling.PositionToRefAndAltHaplotypes
-
- getMapFromFasta(alternativeSeqFile) - Static method in class net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
-
Load a fasta file in a map, headers are keys and sequences are values assumes a fasta file in which sequences are not breaked between lines
- getMapFromFasta(IBDsequences) - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
-
- getMappedReads() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary
-
- getMapPositionsInRanges() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Create map of ReferenceRange ids to list of provided positions
in that range.
- getMapType() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- getMaxNodesPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
ranges with more nodes will not be used
- getMaxParents() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getMaxReadsPerKB() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
ranges with more reads per kb will not be used
- getMaxReadsPerKB() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- getMaxReadsPerKB() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getMeanDel() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getMeanDepth(gvcfFile) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
-
Simple method to compute the mean of the depths.
- getMeanDepth(gvcfFile, intervalFile) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
-
- getMeanIndel() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getMeanIns() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getMedianDepth(gvcfFile) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
-
Simple method to calculate the Median depth for a GVCF file.
- getMedianDepth(gvcfFile, intervalFile) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
-
- getMethodDescriptionFromName(method_name) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Method queries the db methods table for the description field given a methods name
- getMethodDescriptionFromName(method_name) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getMethodDetails() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- getMethodIdFromName(method_name) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns method_id given a method name. or 0 if no id found for the given name
- getMethodIdFromName(method_name) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getMethodIdFromNames(dbConn, methodList) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPluginKt
-
- getMethodName() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- getMethodName() - Method in class net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord
-
- getMinCoverage() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getMinEditDistances() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary
-
- getMinProbability() - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- getMinReadsPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
ranges with fewer reads will not be used
- getMinReadsPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- getMinReadsPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getMinTaxaPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getMinTransitionProbability() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
the minimum transition probability
- getMinTransitionProbability() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
the minimum transition probability that will be returned
- getMissingDepth() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- getMissingPL() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- getModeDepth(gvcfFile) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
-
Simple method to get the mode of the depth.
- getModeDepth(gvcfFile, intervalFile) - Static method in class net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianAnnotation
-
- getMostProbableIntegerStateSequence() - Method in class net.maizegenetics.pangenome.hapCalling.ViterbiForDiploidPath
-
- getMultiset() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdMultiset
-
- getMyAltAllele() - Method in class net.maizegenetics.pangenome.api.DBVariant
-
- getMyAncestralID() - Method in class net.maizegenetics.pangenome.api.DBVariant
-
- getMyChromosome() - Method in class net.maizegenetics.pangenome.api.DBVariant
-
- getMyChromosome() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- getMyEnd() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- getMyGraph() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
the HaplotypeGraph to be used for path finding
- getMyGraph() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
the HaplotypeGraph used for imputation
- getMyGraph() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getMyID() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- getMyLogger() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
- getMyLogger() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
- getMyLogger() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
- getMyMethods() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- getMyParentList() - Method in class net.maizegenetics.pangenome.hapCalling.MostLikelyParents
-
- getMyParentToHapidMap() - Method in class net.maizegenetics.pangenome.hapCalling.MostLikelyParents
-
- getMyPathMethod() - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
- getMyPathMethod() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
- getMyRefAllele() - Method in class net.maizegenetics.pangenome.api.DBVariant
-
- getMyReferenceName() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- getMyRefSequence() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
- getMyStart() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- getMyStartPosition() - Method in class net.maizegenetics.pangenome.api.DBVariant
-
- getMyTaxaList() - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
- getMyTaxaList() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
- getMyTransitionMatrix() - Method in class net.maizegenetics.pangenome.hapCalling.ViterbiForDiploidPath
-
a
- getMyVariantID() - Method in class net.maizegenetics.pangenome.api.DBVariant
-
- getName() - Method in class net.maizegenetics.pangenome.api.Method
-
- getName() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- getNM() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- getNodeList() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
an list containing for each
- getNodeList() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileInput
-
- getNodePairList() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
- getNodeTree() - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
A map of ReferenceRange
- getNoReadProbabilityMap() - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- getNthreads() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
- getNumAlignedBases(asmCoordSet) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- getNumberOfObservations() - Method in class net.maizegenetics.pangenome.hapCalling.ViterbiForDiploidPath
-
The number of reference ranges
- getNumberOfStates() - Method in class net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
-
- getNumberOfStates() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
- getNumberOfTaxaNames() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbabilityWithInbreeding
-
- getNumDel() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getNumIndels() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getNumIndels() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- getNumIns() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- getNumReads() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getNumSNPs() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- getOutDir() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
- getOutExt() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
- getOutputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- getOverlappingEntriesFromGff(contig, haplotypeRange, asmCenterGffs) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Search the gff entry map for overlaps with the haplotypeNode asm coordinates.
Requires as input a map keyed by TASSEL Position object as well as the contig
and coordinates from the haplotypeNode.
- getPairedSimilarFragmentsFromMummer(mummerAlignments) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.SyntenicAnchors
-
Grab the ref and asm start/end positions, determine asm strand direction, calculate a score, and store all to a list of PairedSimilarFragments The score is calculated as: (%id * asmLen)/100 casted to int
- getPairList() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileResult
-
- getParentFinder() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getPath() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- getPath() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- getPathIdsForReadMappingIds(readMappingIds) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns path_ids from the read_mapping_paths table associated with the list of read_mapping_ids provided.
- getPathIdsForReadMappingIds(readMappingIds) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getPathsForTaxonMethod(taxon, method_name) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Method takes a list of taxa and a method name and returns the paths (if populated in the paths table) stored for each taxon/method pair. For each taxon, a List> is returned, which provides a haplotypes_id list for taxon's chromosome. There will be only 1 list if it is a haploid, 2 for a diploid, etc
- getPathsForTaxonMethod(taxon, method_name) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getPCorrect() - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
The probability that a read has been aligned correctly
- getPhgAccess() - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingDecoder
-
- getPluginsToGetParams() - Method in class net.maizegenetics.pangenome.pipeline.MakeDefaultDirectoryPlugin
-
- getPosition() - Method in class net.maizegenetics.pangenome.hapcollapse.RefAltData
-
- getPositionToRefAndAltIdsMap() - Method in class net.maizegenetics.pangenome.hapCalling.PositionToRefAndAltHaplotypes
-
- getPreviousNodePairList() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
- getProbabilityCorrect() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
the probability that a read has aligned correctly
- getProbabilityCorrect() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidEmissionProbability
-
the probability that a read was aligned to the right place
- getProbCorrect() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- getProbCorrect() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getProbObservationGivenState() - Method in class net.maizegenetics.pangenome.hapCalling.ViterbiForDiploidPath
-
an
- getProbObsGivenState(haplotype, refRange) - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- getProbObsGivenState(state, obs, node) - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- getProbObsGivenState(state, anchor) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
-
- getProbObsGivenState(state, obs, node) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
-
- getProbObsGivenState(state, rangeIndex) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidEmissionProbability
-
Returns the emission probability for a given state index and range index.
The range index is the zero-based index into the ordered list of ranges for a HaplotypeGraph.
The state index is the zero-based index into an ordered list of states, where each state is an ordered pair
of HaplotypeNodes returned by the method
nodePairs. The emission probability for a given node pair is calculated
by the method
nodePairProbabilityList.
- getProbObsGivenState(state, obs, node) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidEmissionProbability
-
Calls getProbObsGivenState(state, rangeIndex) where rangeIndex = node.
The value of obs is not used.
- getPseudoGenomeGFFCoordinates(asmGffRange, hapNodeRange, offset) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Creates new start/end coordinates based on the parts of the haplotype node that intersect
with the range for an assembly GFF3 entry. When calculating the new coordinates, the range
overlaps and the offset from the start of the pseudo-genome are considered.
- getPTrue() - Method in class net.maizegenetics.pangenome.hapCalling.ViterbiForDiploidPath
-
the initial state probabilities for the states at the first reference range
- getPurgeArray() - Method in class net.maizegenetics.pangenome.hapCalling.KmerToRefRangeIdToPurgeArray
-
- getQueryName() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- getRange(start, end, trim) - Static method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPluginKt
-
Standardizes the format of the ranges: closed on lower edge, open on top
This is mostly to make sure that concatenating two adjacent ranges
Produces one large range.
Also handles trimming some amount off of the end of the range
And flipping ranges where start > end
- getRangesForChrom(refRangeMap, chrom, anchorType) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- getRangesForChrom(refRangeMap, chrom, anchorType) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- getRangeToNodes() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidEmissionProbability
-
a map of
- getReadCountFromSam(samFile) - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
- getReadHapids() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
a Multimap of
- getReadHapids() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidEmissionProbability
-
a Multimap of
- getReadMap() - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
A Multimap of ReferenceRange
- getReadMap() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- getReadMappingCounts() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingInput
-
- getReadMappingCounts() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingInput
-
- getReadMappingId(line_name, method_name, file_group_name) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Method uses line_name, method_name and file_Group_name to fetch a read_mapping_id. -1 returned if the this combination is not present in the db.
- getReadMappingId(line_name, method_name, file_group_name) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getReadMappingId() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- getReadMappingIdsForTaxaMethod(taxa, method) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
This method takes a list of taxa and a method name. It returns a list of read_mapping Ids based on these 2 parameters
- getReadMappingIdsForTaxaMethod(taxaList, method) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getReadMappings() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- getReadMappingsForId(readMappingId) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Method to get the Read Mapping data from the DB using the read_mapping_id. Generally this is returned from PHGData.getReadMappingId(String line_name, String method_name, String file_group_name)
- getReadMappingsForId(readMappingId) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getReadMappingsForMethod(methodName) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Method to get the mapping ids by method
- getReadMappingsForMethod(methodName) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getReadName() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- getReadName() - Method in class net.maizegenetics.pangenome.hapCalling.SingleHapMapping
-
- getRefAllele() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getRefDepth() - Method in class net.maizegenetics.pangenome.hapcollapse.RefAltData
-
- getRefDepth() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- getRefEndPos() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- getReferenceRange() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
-
- getRefFasta() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- getRefFasta() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- getRefLineName(database) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Returns the line name of the reference genotype
- getRefName() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- getRefPL() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- getRefRange() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileInput
-
- getRefRange() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileResult
-
- getRefRangeId() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getRefRangeId() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- getRefRangeIdArray() - Method in class net.maizegenetics.pangenome.hapCalling.KmerToRefRangeIdToPurgeArray
-
- getRefRangeIDFromString(refData) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns reference range id
- getRefRangeIDFromString(refData) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getRefRanges() - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- getRefRangesForMethod(methodName) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Method to return all reference ranges associated with a specified method name
- getRefRangesForMethod(methodName) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getRefRangeToHapIdMap() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- getRefRangeToHapidMap(graph) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
- getRefRecord() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.MAFRecord
-
- getRefSamOutFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- getRefStartPos() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- getRegionCoverage(rangeSet, targetRange) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
This method takes a RangeSet of integers, and a single range. It finds all the ranges in the set that intersect the targetRange. Calculate both the number of bases from the targetRange that are represented in the rangeSet, and the percentage of the bases represented. Return a Tuple with this information.
- getRegionCoverage(rangeSet, targetRange) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- getREMAINING_INFOS_KEY() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
- getRemoveAdapter() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
- getRemoveEqual() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- getRemoveEqual() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getRemoveRangesWithEqualCounts() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
ranges for which all hapid sets have the same count will not be used
- getRequiredTaxaList() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getSameGameteProbability() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- getSameGameteProbability() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getSAMStats(samFile) - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
Given a sam or bam file, return the following as an AlignmentSummary object:
number of aligned reads
number of unaligned reads
list of the minimum edit distance for each aligned read
When the sam file contains multiple alignments (i.e. secondary alignments), we get the edit distance for each
alignment and then choose the lowest to add to the list.
- getScore() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.MAFRecord
-
- getScore() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- getSequence() - Method in class net.maizegenetics.pangenome.api.RPHGMethodsKotlin.HaplotypeSequences
-
- getSize() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- getSmallFactorials() - Static method in class net.maizegenetics.pangenome.hapCalling.FindBestDiploidPathKt
-
- getSNPsFromVCF(vcfFile) - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Method to retrieve the SNPs from the VCF file. We need to do this in order to map SNPs to haplotype nodes.
- getSNPToHapIdMapping(refAndHapPair, snpsInRefRange, snpMap) - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Method to get Mappings from SNP -> HapId Lists
We only support the first non-reference allele for simplicity
- getSplitNodes() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
should nodes with more than one taxon be split into nodes of one taxon each
- getSplitTransitionProb() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath
-
the probability of a node given that the previous node was the same taxon or 1
- getStart() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin.RefrangeInfo
-
- getStart() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- getStart() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- getStart() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.RefRangeData
-
- getStart() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- getStartEndCoordinates(entry, ref) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Find the start/end coordinates from a tab-delmimited Mummer4 coords file entry
- getStartPos() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- getStartPosition() - Method in class net.maizegenetics.pangenome.hapCalling.SecondaryStats
-
- getStartPositions() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- getStepSize() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- getStrand() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- getStrand() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- getStrand() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- getTaxaForPathMethod(method_name) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Method to get a list of all genoid line_names that have paths for method = method_name.
- getTaxaForPathMethod(method_name) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getTaxaForTaxaGroup(group_name) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Get the taxa that make up the specified taxa group
- getTaxaForTaxaGroup(group_name) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getTaxaGroupIDFromName(group_name) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns taxa_grp_id given a taxa group name. or 0 if no id found for the given name
- getTaxaGroupIDFromName(group_name) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getTaxonName() - Method in class net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord
-
- getTaxonPathsForMethod(method_name) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Returns a map of taxon to paths for that taxon from the paths table for a specified method name.
- getTaxonPathsForMethod(method_name) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- getTaxonToGffFileMap(keyFile) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Reads a key file with columns for "taxon" and "Path/name of gff file"
Returns a map of taxon->fileName
- getToolTipText() - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.api.MethodTableReportPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.api.ReadMethodTablePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.api.ReferenceRangeSummaryPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.api.WriteGraphAsGFAPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.ChangeDBMethodTypePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeleteReadMappingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.RankingFilePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.io.PathsToFastaPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipeline.MakeDefaultDirectoryPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipeline.MakeInitialPHGDBPipelinePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
- getToolTipText() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
- getTotalAlignedBps() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getTotalBases() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- getTotalD() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getTotalDeletes() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- getTotalDP() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- getTotalEQ() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getTotalEQ() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- getTotalHClip() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getTotalI() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getTotalInserts() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- getTotalM() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- getTotalNM() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getTotalReadBps() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getTotalReadLength() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- getTotalReads() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- getTotalReads() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- getTotalRefLength() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- getTotalSClip() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getTotalSNP() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- getTotalX() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- getTransitionProbability(state1, state2) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
-
- getTransitionProbability(state1, state2) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
- getType() - Method in class net.maizegenetics.pangenome.api.Method
-
- getType() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- getType() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- getUnmappedReads() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary
-
- getUseLikelyParents() - Method in class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- getValidFiles() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
- getValue() - Method in enum net.maizegenetics.pangenome.db_loading.DBLoadingUtils.GenomeFileType
-
- getValue() - Method in enum net.maizegenetics.pangenome.db_loading.DBLoadingUtils.MethodType
-
- getVariantContextFromHaplotypeNodeList(nodeList) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
Method to extract the VCF VariantContexts from a List of HaplotypeNodes
- getVariantContextFromHaplotypePath(bestPath) - Static method in class net.maizegenetics.pangenome.hapCalling.HapCallingUtils
-
Method to extract the VCF VariantContexts from the HaplotypePath. TODO remove if we get rid of HaplotypePath
- getVariantContextMap() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- getVariantData(chrom, alleleHashMap, vi, dbConn) - Static method in class net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
-
Method will return a Tuple of the hash of (chrom, start_position, refAlleleID, altAlleleID) and a VariantMappingData record The alleleHashMap should contain the initial alleles pre-populated. If the alleleId cannot be found from this hash map, the db will be queried. Generally 2/3 of all alleles will be found on the hashmap.
- getVariantId() - Method in class net.maizegenetics.pangenome.hapcollapse.RefAltData
-
- getVCFStats(file) - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
Calculates summary statistics for the given gvcf file and returns them as a map
- getVcList() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.ResultChannelData
-
Deprecated.
- gffAllIDcount(gffSet, count) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Takes a set of Gff3Features, creates a mapping of
GFF id (ID from the attributes column) to number of times it appears
The "count" parameter tells by what amount to shorten the ID.
- gffFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
Tab delimited .txt file containing gene-only GFF data from reference GFF file for all desired chromosomes,
- gffFile(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
Set Gene File. Tab delimited .txt file containing gene-only GFF data from reference GFF file for all desired chromosomes,
- gffFile() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
GFF file holding the genic and intergenic regions.
- gffFile(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set GFF file. GFF file holding the genic and intergenic
regions.
- gffFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Reference GFF3 file used to create the CDS fasta for
minimap2 alignment
- gffFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Set Ref GFF3 File. Reference GFF3 file used to create
the CDS fasta for minimap2 alignment
- gffOutputDir() - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
If present, gff files will be written to this directory.
- gffOutputDir(value) - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
Set GFF Output Directory. If present, gff files will
be written to this directory.
- gffSingleIDcount(idToMatch, gffSet) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Counts the number of times a single GFF ID appears.
User may specify the full ID or just part of it. The
code checks for GFF entries where the ID contains the
user specified string.
- GFFUtilsKt - Class in net.maizegenetics.pangenome.annotations
-
- graph(configFile, methods, numRangesPerQuery, includeSequence, includeVariants, localGVCFFolder) - Static method in class net.maizegenetics.pangenome.api.HaplotypeGraphStream
-
This returns a streams sets of haplotype nodes paired with their reference range.
The nodes included are defined by the haplotype method(s) / reference range group method(s)
provided. The nodes can either include of exclude the sequences and variants (for memory
efficiency). The database connection information is specified in the config file.
- graphExportBasename() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
The base name for R-igraph export files. If a value is supplied, vertices, edges, and a layout will be exported.
- graphExportBasename(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Graph Export. The base name for R-igraph export files. If a value is supplied, vertices, edges, and a layout will be exported.
- GraphIdMaps - Class in net.maizegenetics.pangenome.hapCalling
-
Class to hold the 4 pieces of information which are needed for readMapping.
Using Jackson this class can be serialized into JSON
- GraphIdMaps(hapIdToRefRangeMap, hapIdToLengthMap, refRangeToHapIdMap, haplotypeListId, hapIdToTaxaList) - Constructor for class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
Class to hold the 4 pieces of information which are needed for readMapping.
Using Jackson this class can be serialized into JSON
- GraphIdMapsKt - Class in net.maizegenetics.pangenome.hapCalling
-
- GraphIO - Class in net.maizegenetics.pangenome.api
-
- GraphSpliterator - Class in net.maizegenetics.pangenome.api
-
This Spliterator class is the bases to create the haplotype node stream for the {@link #graph(String, List
>, Boolean, Boolean) graph}
- GraphSpliterator(database, methods, numRangesPerQuery, includeSequence, includeVariants, localGVCFFolder) - Constructor for class net.maizegenetics.pangenome.api.GraphSpliterator
-
This Spliterator class is the bases to create the haplotype node stream for the {@link #graph(String, List
>, Boolean, Boolean) graph}
- GraphToGenotypeTable - Class in net.maizegenetics.pangenome.api
-
- graphToHapsInRefRangeVectors(graph, refRanges, includeSequence, includeVariants) - Static method in class net.maizegenetics.pangenome.pipelineTests.GenerateRForPHG
-
Given a PHG HaplotypeGraph, create a set of vectors representing data for all Haplotypes/Nodes in the graph. This assumes the graph was created with sequence and variant info if the user has these 2 parameters as "true"
- graphToRefRangeVectors(graph, refRanges) - Static method in class net.maizegenetics.pangenome.pipelineTests.GenerateRForPHG
-
Given a PHG HaplotypeGraph, create a set of vectors representing data for all ReferenceRanges in the graph. If the user passes a list of refRangeIds, then only return data for those reference ranges. If this list is null or empty, return data for all reference ranges in the graph.
- GraphUtils - Class in net.maizegenetics.pangenome.api
-
- groupMethods() - Method in class net.maizegenetics.pangenome.api.ReferenceRange
-
Returns group methods that this range belongs.
- groupName() - Method in class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPlugin
-
Name for this taxa group.
- groupName(value) - Method in class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPlugin
-
Set Taxa Group Name. Name for this taxa group.
- gtvalues - Static variable in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
- gvcf() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- GVCFBedfileMetricPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This class contains a plugin that will take GVCF files together with bedfile defined intervals
and create a metrics file showing data on the interval chrom/start/end/len, the length of this interval
for each taxa based on GVCF information, how much of each interval is covered by each GVCF taxa.
- GVCFBedfileMetricPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
This class contains a plugin that will take GVCF files together with bedfile defined intervals
and create a metrics file showing data on the interval chrom/start/end/len, the length of this interval
for each taxa based on GVCF information, how much of each interval is covered by each GVCF taxa.
- GVCFBedfileMetricPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
This class contains a plugin that will take GVCF files together with bedfile defined intervals
and create a metrics file showing data on the interval chrom/start/end/len, the length of this interval
for each taxa based on GVCF information, how much of each interval is covered by each GVCF taxa.
- GVCFBedfileMetricPlugin.ChromosomeGVCFRecord - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- GVCFBedfileMetricPluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- gvcfDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- gvcfDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- gVCFDirectory() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Directory holding all the gvcf files
- gVCFDirectory(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Set Gvcf Dir. Directory holding all the gvcf files
- gvcfDirectory() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
Local directory holding all the gvcf files that were
processed into haplotypes for the database.
- gvcfDirectory(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
Set Gvcf Directory. Local directory holding all the
gvcf files that were processed into haplotypes for
the database.
- gVCFDirectory() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
Directory holding all the gvcf files.
- gVCFDirectory(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
Set Gvcf Dir. Directory holding all the gvcf files.
- gvcfFileID() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
- gvcfFileId() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- gvcfFileNameToHash(database) - Static method in class net.maizegenetics.pangenome.api.VariantUtils
-
This method returns a map of a gvcf file name (NOT full path) to that file's stored hash value. This can be used to verify that files with this name already stored to a local gvcf folder have the same hash as the file referenced in the table.
- GVCFGenotypeSequence - Class in net.maizegenetics.pangenome.fastaExtraction
-
GVCFGenotypeSequence This class should be used instead of GVCFSequence when you want to have diploid calls being returned. Due to the fact that this class will return diploids, you cannot query a range of positions as we cannot separate the two gametes. If you need a range, you will have to loop through each position and retrieve them one at a time.. The Diploids are separated by the / character
- gvcfIdsToGvcfFileMap(database) - Static method in class net.maizegenetics.pangenome.api.VariantUtils
-
This method returns all the gvcf file entries from the genome_file_data table. These are the entries with type=2 (type=1 are assemblies)
- gvcfIdToFilePath() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
- gVCFInputDir() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
Directory holding the GVCF files to be filtered.
- gVCFInputDir(value) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
Set Gvcf Dir. Directory holding the GVCF files to be filtered.
- gVCFKeyFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
Keyfile used to specify the inputs to the DB. Must
have columns sample_name, files. Ordering of the columns
does not matter.
sample_name is the name of the taxon you are uploading.
files is a comma-separated list of file names(without
path) providing the names of the GVCF files to be uploaded.
- gVCFKeyFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
Set GVCF Key File. Keyfile used to specify the inputs
to the DB. Must have columns sample_name, files. Ordering
of the columns does not matter.
sample_name is the name of the taxon you are uploading.
files is a comma-separated list of file names(without
path) providing the names of the GVCF files to be uploaded.
- gVCFOutput() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Output GVCF file
- gVCFOutput(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Set Gvcf Output. Output GVCF file
- gVCFOutputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Directory for gvcf files to be output for later use
- gVCFOutputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Set GVCF Output Dir. Directory for gvcf files to be
output for later use
- gVCFOutputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Directory for gvcf files to be output for later use
- gVCFOutputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Set GVCF Output Dir. Directory for gvcf files to be output for later use
- GVCFSequence - Class in net.maizegenetics.pangenome.fastaExtraction
-
GVCFSequence.java
- GVCFSequence() - Constructor for class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- gvcfServerPath() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
semi-colon separated server and path, e.g. myserver.com;/path/to/gvcfs.
If no semi-colon and only the path is present, the
gvcf files will be copied to that path on the the current
server.
.
- gvcfServerPath(value) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Set Gvcf Server Path. semi-colon separated server and
path, e.g. myserver.com;/path/to/gvcfs. If no semi-colon
and only the path is present, the gvcf files will be
copied to that path on the the current server.
.
- gvcfServerPath - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- GVCFStats - Class in net.maizegenetics.pangenome
-
- GVCFTyperPlugin - Class in net.maizegenetics.pangenome.hapcollapse
-
Deprecated.
- GVCFTyperPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
- GVCFTyperPlugin.EMIT_MODE - Enum in net.maizegenetics.pangenome.hapcollapse
-
Deprecated.
- GVCFUtils - Class in net.maizegenetics.pangenome.hapcollapse
-
Created by zrm22 on 9/6/17.
- GZipCompression - Class in net.maizegenetics.pangenome.db_loading
-
Examples from https://stackoverflow.com/questions/16351668/compression-and-decompression-of-string-data-in-java
and : https://myadventuresincoding.wordpress.com/2016/01/02/java-simple-gzip-utility-to-compress-and-decompress-a-string/
Class used to compress strings for memory efficient storage to db.
- id() - Method in class net.maizegenetics.pangenome.api.AlleleInfo
-
- id() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
- id() - Method in class net.maizegenetics.pangenome.api.ReferenceRange
-
Identifier for a unique reference range
- id() - Method in class net.maizegenetics.pangenome.api.Variant
-
- ignoreWarnings() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Ignore Warnings when checking number of reads per unmerged
file. If this is enabled, this will write to the DB
even though there may be errors.
- ignoreWarnings(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Ignore Warnings. Ignore Warnings when checking
number of reads per unmerged file. If this is enabled,
this will write to the DB even though there may be
errors.
- ImportDiploidPathPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
- ImportDiploidPathPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin
-
- ImportDiploidPathPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin
-
- ImportHaplotypePathFilePlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Deprecated.
- ImportHaplotypePathFilePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
-
Deprecated.
- importKmerToHapIdMapFromBinaryFile(fileName) - Static method in class net.maizegenetics.pangenome.hapCalling.KmerUtils
-
- importKmerToHapIdMapFromTextFile(fileName) - Static method in class net.maizegenetics.pangenome.hapCalling.KmerUtils
-
Import the KmerToHapIdMap from a text file. This will read from a file with the format:
kmerAsLong\tHapId1\tHapId2\tHapId3.....
- importKmerToIntMap(fileName) - Static method in class net.maizegenetics.pangenome.hapCalling.KmerUtils
-
- importReadMapping(inputFileName) - Static method in class net.maizegenetics.pangenome.hapCalling.ReadMappingUtils
-
Function to read in the Readmapping file into a Map
- ImportReadMappingToDBPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
This plugin will open up a connection to a DB which multiple sub DBs will need to be merged to.
- ImportReadMappingToDBPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
This plugin will open up a connection to a DB which multiple sub DBs will need to be merged to.
- ImportReadMappingToDBPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- ImputePipelinePlugin - Class in net.maizegenetics.pangenome.pipeline
-
- ImputePipelinePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
- ImputePipelinePlugin() - Constructor for class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
- ImputePipelinePlugin.IMPUTE_TASK - Enum in net.maizegenetics.pangenome.pipeline
-
- ImputePipelinePlugin.INPUT_TYPE - Enum in net.maizegenetics.pangenome.pipeline
-
- ImputePipelinePluginKt - Class in net.maizegenetics.pangenome.pipeline
-
- imputeTarget() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Specifies the target or desired endpoint when running
the plugin. For any given endpoint, the plugin will
check that all required previous step have been completed
and run those as needed.
- imputeTarget(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Impute Target. Specifies the target or desired
endpoint when running the plugin. For any given endpoint,
the plugin will check that all required previous step
have been completed and run those as needed.
- inbreedingCoef() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
The coefficient of inbreeding, f, for the taxa being
imputed.
- inbreedingCoef(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Inbreed Coef. The coefficient of inbreeding, f,
for the taxa being imputed.
- includeSequences() - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
Whether to include sequences in haplotype nodes.
- includeSequences(value) - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
Set Include Sequences. Whether to include sequences
in haplotype nodes.
- includeSequences() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Whether to include sequences in haplotype nodes.
- includeSequences(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Set Include Sequences. Whether to include sequences in haplotype nodes.
- includeSequences() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
Whether to include sequences in haplotype nodes.
- includeSequences(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
Set Include Sequences. Whether to include sequences
in haplotype nodes.
- includeVariantContexts() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Whether to include variant contexts in haplotype nodes.
- includeVariantContexts(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Set Include Variant Contexts. Whether to include variant contexts in haplotype nodes.
- includeVariantContexts() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
Whether to include variant contexts in haplotype nodes.
- includeVariantContexts(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
Set Include Variant Contexts. Whether to include variant
contexts in haplotype nodes.
- inclusionCountMap(inclusionCounts) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
-
- inclusionFilename() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
The name of the file containing read inclusion and exclusion counts for hapids.
- inclusionFilename(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Inclusion File. The name of the file containing read inclusion and exclusion counts for hapids.
- inclusionFilenameDir() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
The name of the file containing read inclusion and exclusion counts for hapids.
- inclusionFilenameDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Set Inclusion File Dir. The name of the file containing read inclusion and exclusion counts for hapids.
- inclusionFilenameDir() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
The name of the file containing read inclusion and exclusion counts for hapids.
- inclusionFilenameDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
Set Inclusion File Dir. The name of the file containing read inclusion and exclusion counts for hapids.
- IndelDistributions(numIndels, meanIndel, indelLowerQuartile, indelMedian, indelUpperQuartile, indelLargest, numIns, meanIns, insLowerQuartile, insMedian, insUpperQuartile, insLargest, numDel, meanDel, delLowerQuartile, delMedian, delUpperQuartile, delLargest) - Constructor for class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
Data class containing summary information about indel distribution (number of insertions/deletions, average sizes, etc.)
toString() is overridden in order to make printing to tab-delimited summary file easier
- indelFile() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
Optional file to write all indel lengths to
If not provided, indel lengths will not be written
Each line begins with the gvcf and chromosome name (separated by underscore)
And then the indel sizes, separated by tabs
- indelFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
Set indel file
Optional file to write all indel lengths to
If not provided, indel lengths will not be written
Each line begins with the gvcf and chromosome name (separated by underscore)
And then the indel sizes, separated by tabs
- indexFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Name of the indexFile file to process
- indexFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Set Minimap2 index file for pangenome. Name of the
indexFile file to process
- indexFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Name of the indexFile file to process
- indexFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Minimap2 index file for pangenome. Name of the
indexFile file to process
- indexFile() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Name of the indexFile file to for writing to scriptTemplate.
If not specified, will be written to the
script and will need to be updated.
- indexFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set Minimap2 index file for pangenome. Name of the
indexFile file to for writing to scriptTemplate. If
not specified, will be written to the script
and will need to be updated.
- indexFile() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Name of the SNP to HapIdList index file created by
IndexHaplotypesBySNPPlugin
- indexFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Set Index File. Name of the SNP to HapIdList index
file created by IndexHaplotypesBySNPPlugin
- IndexHaplotypeKmersPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Deprecated.
- IndexHaplotypeKmersPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
- IndexHaplotypesBySNPPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Class to index the PHG by the SNP values contained within.
The output is a file in the form:
refRangeId chr position refAllele altAllele refHapIds altHapIds
1 1 24 A T 102,104 103
1 1 95 C T 103,104 102
1 1 101 G T 103,104 102
- IndexHaplotypesBySNPPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Class to index the PHG by the SNP values contained within.
The output is a file in the form:
refRangeId chr position refAllele altAllele refHapIds altHapIds
1 1 24 A T 102,104 103
1 1 95 C T 103,104 102
1 1 101 G T 103,104 102
- IndexHaplotypesBySNPPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Class to index the PHG by the SNP values contained within.
The output is a file in the form:
refRangeId chr position refAllele altAllele refHapIds altHapIds
1 1 24 A T 102,104 103
1 1 95 C T 103,104 102
1 1 101 G T 103,104 102
- IndexHaplotypesBySNPPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- IndexKmerByHammingPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Deprecated.
- IndexKmerByHammingPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
create fullGenomeKmerToRefIdMap mutable map:call createKmerToRefRangeMap() with the mutable map from above.
- indexKmerLength() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Minimap2 index parameter k, the kmer length of the
minimizers, which is used to index the pangenome.
- indexKmerLength(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Index Kmer Length. Minimap2 index parameter k,
the kmer length of the minimizers, which is used to
index the pangenome.
- indexKmersPrefix() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Prefix to keep kmers that start with that prefix.
This is to reduce the number of Kmers by 1/4
- indexKmersPrefix(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Set Kmer Prefix. Prefix to keep kmers that start with
that prefix. This is to reduce the number of Kmers
by 1/4
- indexNumberBases() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Minimap2 index parameter I, the maximum number of bases
loaded into memory, which is used to index the pangenome.
This must be large enough to hold the entire pangenome
in memory.
- indexNumberBases(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Index Number Bases. Minimap2 index parameter I,
the maximum number of bases loaded into memory, which
is used to index the pangenome. This must be large
enough to hold the entire pangenome in memory.
- indexOfNonGapCharacters(seq, start, end) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MafUtils
-
- indexWindowSize() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Minimap2 index parameter w, the minimizer window size,
which is used to index the pangenome.
- indexWindowSize(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Index Window Size. Minimap2 index parameter w,
the minimizer window size, which is used to index the
pangenome.
- inDir() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
Input directory path
- inExt() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
File extension of FASTQCOL files
- initialize() - Method in class net.maizegenetics.pangenome.hapCalling.ViterbiForDiploidPath
-
- input() - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
-
Input VCF file
- input(value) - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
-
Set Input. Input VCF file
- inputASMFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
Input Assembly file
- inputASMFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
Set Input file. Input Assembly file
- InputChannelData(refFasta, asmFasta, asmDBName, chrom, asmServer, asmFullGenomeFasta) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- InputChannelData(refFasta, asmFasta, asmDBName, outputDir, gffFile, refSamOutFile) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- inputConsensusHaplotypeMethod() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Methods needed to populate a PHG object in order to
create consensus on. If left blank a method will be
auto-generated based on asmMethodName and wgsMethodName.
If either are not set only one will be used.
- inputConsensusHaplotypeMethod(value) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Set Input Consensus Methods. Methods needed to populate
a PHG object in order to create consensus on. If left
blank a method will be auto-generated based on asmMethodName
and wgsMethodName. If either are not set only one
will be used.
- inputDir() - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
Directory with files of haplotypes reference ranges
- inputDir(value) - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
Set Input Dir. Directory with files of haplotypes reference
ranges
- inputDir() - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Directory holding the input files. This can either
be DB config files or can be flat read mapping files
- inputDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Set Input Mapping Dir. Directory holding the input
files. This can either be DB config files or can be
flat read mapping files
- inputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
Path for directory holding the files to be changed
- inputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
Set Input Directory. Path for directory holding the
files to be changed
- inputDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- inputDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- inputFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
GVCF File to be filtered.
- inputFile(value) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
Set Input G V C F File. GVCF File to be filtered.
- inputFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Input of the first Fastq file to be run through. If
the keyfile has a pair it will pick it up correctly.
If this is not set it will run everything in the inputDir
- inputFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Input Fastq File. Input of the first Fastq file
to be run through. If the keyfile has a pair it will
pick it up correctly. If this is not set it will run
everything in the inputDir
- inputFile() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Input Multisample SAM file to be run through. If this
is not set it will run everything in the inputDir
- inputFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Input S A M File. Input Multisample SAM file to
be run through. If this is not set it will run everything
in the inputDir
- inputFile() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Input SAM file to be run through. If this is not set
it will run everything in the inputDir
- inputFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set Input S A M File. Input SAM file to be run through.
If this is not set it will run everything in the inputDir
- inputFileDirectory() - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
-
Deprecated.
Input file directory
- inputFileDirectory(value) - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
-
Deprecated.
Set Input File Directory. Input file directory
- inputGVCFDir() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
Input gvcf directory.
- inputGVCFDir(value) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
Set Input GVCF Directory. Input gvcf directory.
- inputIntervalFile() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
Input interval file to run GVCFTyper with.
- inputIntervalFile(value) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
Set Input Interval File. Input interval file to run GVCFTyper with.
- inputKeyFile() - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
Name of the inputKeyFile file to process.
- inputKeyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
Set Input Key File. Name of the inputKeyFile file to
process.
- inputKeyFile() - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
Name of the inputKeyFile file to process.
- inputKeyFile(value) - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
Set Input Key File. Name of the inputKeyFile file to
process.
- inputPAFFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPlugin
-
Input PAF file
- inputPAFFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPlugin
-
Set Input PAF file. Input PAF file
- inputType() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
The type of data to be used for imputation
- inputType(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Input Type. The type of data to be used for imputation
- insertLength() - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
for paired end reads the number of base pairs between
reads
- insertLength(value) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
Set Insert Length. for paired end reads the number
of base pairs between reads
- INSTANCE - Static variable in class net.maizegenetics.pangenome.db_loading.GZipCompression
-
Examples from https://stackoverflow.com/questions/16351668/compression-and-decompression-of-string-data-in-java
and : https://myadventuresincoding.wordpress.com/2016/01/02/java-simple-gzip-utility-to-compress-and-decompress-a-string/
Class used to compress strings for memory efficient storage to db.
- instance(refFileName, gvcfFileName) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
Returns an initialized GVCFSequence given the input Reference and GVCF Files.
- instance(referenceSequence, gvcfFileName) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
Returns an initialized GVCFSequence given the input Reference and GVCF Files. This should be used if you are running multiple GVCFs through using the same Reference File. Currently will speed up processing each GVCF by about a minute.
- instance(referenceSequence, gvcfFileName, missingAsRef) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
Instance method to allow for reference filling in missing for a file
- instance(referenceSequence, variantContexts, missingAsRef, taxonName) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
Instance method to build the GenomeSequence in memory using a List of VariantContexts
- instance(refFileName, gvcfFileName) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Returns an initialized GVCFSequence given the input Reference and GVCF Files.
- instance(referenceSequence, gvcfFileName) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Returns an initialized GVCFSequence given the input Reference and GVCF Files. This should be used if you are running multiple GVCFs through using the same Reference File. Currently will speed up processing each GVCF by about a minute.
- instance(referenceSequence, gvcfFileName, missingAsRef) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Instance method to add in missing as Ref from a file
- instance(referenceSequence, variantContexts, missingAsRef, taxonName) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Instance method to create a GenomeSequenc from a List of VariantContexts
- instance(referenceSequence, variantContexts, missingAsRef) - Static method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- INSTANCE - Static variable in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
- INSTANCE - Static variable in class net.maizegenetics.pangenome.processAssemblyGenomes.MafUtils
-
- intArrayToLong(intPair) - Static method in class net.maizegenetics.pangenome.hapCalling.FindBestDiploidPathKt
-
- INTER_REGION_REFERENCE_RANGE_GROUP - Static variable in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
- interGeneLength() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Number of base pairs to include for each intergenic region
- interGeneLength(value) - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Set Length Of Inter Genes. Number of base pairs to include for each intergenic region
- intergenicStepSize() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
The number of bps that the intergenic split algorithm
will use to step between cut sites
- intergenicStepSize(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Intergenic Step Size. The number of bps that the
intergenic split algorithm will use to step between
cut sites
- interHapDivergence() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Percent each haplotype sequence should diverge from reference
- interHapDivergence(value) - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Set Inter-Haplotype Divergence. Percent each haplotype sequence should diverge from reference
- intervalCoordinates() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- intervalFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
-
Intervals file
- intervalFile(value) - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
-
Set Intervals. Intervals file
- intervalFile() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Interval File used to create the VCF file
- intervalFile(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Interval File. Interval File used to create the VCF file
- intervalsFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
Tab-delimited file containing chrom, interval start position, interval
end position, type
- intervalsFile(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
Set Intervals File. Tab-delimited file containing chrom, intervals
start position, intervals end position, type
end
- intervalsFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Anchor Intervals file to be used when intervals are different than DB, e.g. when using just a small region
- intervalsFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Set Anchor Intervals File. Anchor Intervals file to be used when intervals are different than DB, e.g. when using just a small region
- intervalString() - Method in class net.maizegenetics.pangenome.api.ReferenceRange
-
- is_reference() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
-
- isAltSeqSameAsRefExcludingNs(referenceSeq, alternativeSeq) - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
-
- isCompressed(compressed) - Method in class net.maizegenetics.pangenome.db_loading.GZipCompression
-
- isFileGroupNew(taxon, fileGroupName, methodName) - Method in interface net.maizegenetics.pangenome.db_loading.PHGData
-
Method to check to see if a given taxon and fileGroup are already in the readMapping table of the DB.
- isFileGroupNew(taxon, fileGroupName, methodName) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- isGca() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
GCA fastas have long text as idLines. These fasta will have their id lines specially parsed to extract the chromosome number.
- isGca(value) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
Set Is GCA. GCA fastas have long text as idLines. These fasta will have their id lines specially parsed to extract the chromosome number.
- isIndel() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- isIndel() - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- isKeyEntryInDir(fileNames, currentKeyRecord, fileCol1, fileCol2) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Method to check to see if there are missing files found in the key file but are missing in the Directory.
If they are its ok, we expect the keyfile to have more entries than the directory.
- isPairedEnd() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Flag to set if you are using Paired End reads.
- isPairedEnd(value) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Set Is Paired End. Flag to set if you are using Paired
End reads.
- isPartOf(groupMethod) - Method in class net.maizegenetics.pangenome.api.ReferenceRange
-
Returns whether this reference range is part of specifed group.
- isPhasedAcrossChromosomes() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
-
- isPhasedAcrossGenes() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
-
- isPositionInMap(position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
Simple method to check to see if the position is currently in the map.
- isPositionInMap(position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Simple method to check to see if the position is currently in the map.
- isPositionRefBlock(position) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Simple method to determine if the position in the rangeMap is a Reference Block
- isRefBlock(gvcfRecord) - Static method in class net.maizegenetics.pangenome.api.ConvertVariantContextToVariantInfo
-
Helper function to check to see if a gvcf Record represents a reference block or just a single variant.
- isRefBlock(vc) - Static method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
-
Deprecated.
Simple method to check to see if the Variant is a reference block
- isRefBlock(vc) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Simple method to determine if the current variant context is a reference block or not.
- isReference() - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- isReferenceRecord(currentVC) - Static method in class net.maizegenetics.pangenome.hapcollapse.GVCFUtils
-
Takes a VariantContext record and determines if the data is for a reference range block ro a variant.
- isRefRange(currentVariant) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Simple method to tell if a variantContext is in a reference block in the VCF file. This RefRange is not to be confused with the ReferenceRange object in the PHG api.
- isTestMethod() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Indication if the data is to be loaded against a test method. Data loaded with test methods are not cached with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Is Test Method. Indication if the data is to be loaded against a test method. Data loaded with test methods are not cached with the PHG ktor server
- isTestMethod() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Indication if the data is to be loaded against a test
method. Data loaded with test methods are not cached
with the PHG ktor server
- isTestMethod(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Set Is Test Method. Indication if the data is to be
loaded against a test method. Data loaded with test
methods are not cached with the PHG ktor server
- isVariant() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- isVariant() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- keepHapIDs(graph, hapids) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Filters the given graph to keep only the specified haplotype ids.
- keepHapIdsForSingleRefRange(bestHitMap, hapIdToRangeMap, maxRefRangeError) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Simple function to remobve hapIds if they cross multiple reference ranges.
- keepHapIdsForSingleRefRange(bestHitMap, hapIdToRangeMap, maxRefRangeError) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to keep hapids if they are hitting multiple reference ranges too frequently. If there is a little bit of noise it can be filtered.
- keepRefRangeIDs(graph, rangeIDs) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
- keepRefRanges(graph, ranges) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Creates graph that includes specified reference ranges.
- keyFile() - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
KeyFile file name. Must be a tab separated file using
the following headers:
TaxonName GFF File Path
TaxonName values must match taxon names stored in the
genotypes table.
GFF file path should be full path and file name of
GFF file for the specified taxon
- keyFile(value) - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
Set Key File. KeyFile file name. Must be a tab separated
file using the following headers:
TaxonName GFF File Path
TaxonName values must match taxon names stored in the
genotypes table.
GFF file path should be full path and file name of
GFF file for the specified taxon
- keyFile() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPlugin
-
KeyFile containing taxa that will be deleted. Either
keyFile or taxa must be specified, but not both.
- keyFile(value) - Method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPlugin
-
Set Key File. KeyFile containing taxa that will be
deleted. Either keyFile or taxa must be specified,
but not both.
- keyFile() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeleteReadMappingPlugin
-
Name of the Keyfile to process. Must have columns
cultivar, flowcell_lane, filename, and PlateID.Taxa
names are created from the cultivar column
- keyFile(value) - Method in class net.maizegenetics.pangenome.db_updateDelete.DeleteReadMappingPlugin
-
Set keyFile. Name of the Keyfile to process. Must
have columns cultivar, flowcell_lane, filename, and
PlateID.Taxa names are created from the cultivar column
- keyFile() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
KeyFile file name. Must be a tab separated file using
the following headers:
SampleName ReadMappingIds LikelyParents
ReadMappingIds and LikelyParents need to be comma separated
for multiple values
- keyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set KeyFile. KeyFile file name. Must be a tab separated
file using the following headers:
SampleName ReadMappingIds LikelyParents
ReadMappingIds and LikelyParents need to be comma separated
for multiple values
- keyFile() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
KeyFile file name. Must be a tab separated file using
the following headers:
SampleName ReadMappingIds LikelyParents
ReadMappingIds and LikelyParents need to be comma separated
for multiple values
- keyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set KeyFile. KeyFile file name. Must be a tab separated
file using the following headers:
SampleName ReadMappingIds LikelyParents
ReadMappingIds and LikelyParents need to be comma separated
for multiple values
- keyFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Name of the Keyfile to process. Must have columns
cultivar, flowcell_lane, filename, and PlateID. Optionally
for paired end reads, filename2 is needed. If filename2
is not supplied, Minimap2 will run in single end mode.
Otherwise will be paired.
- keyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set keyFile. Name of the Keyfile to process. Must
have columns cultivar, flowcell_lane, filename, and
PlateID. Optionally for paired end reads, filename2
is needed. If filename2 is not supplied, Minimap2
will run in single end mode. Otherwise will be paired.
- keyFile() - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
KeyFile file name. Must be a tab separated file using
the following headers:
SampleName ReadMappingIds
Additional headers will be ignored. ReadMappingIds
need to be comma separated for multiple values.
If a keyFile is not supplied then all of the read mappings
for the supplied method will be run.
- keyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
Set Key File. KeyFile file name. Must be a tab separated
file using the following headers:
SampleName ReadMappingIds
Additional headers will be ignored. ReadMappingIds
need to be comma separated for multiple values.
If a keyFile is not supplied then all of the read mappings
for the supplied method will be run.
- keyFile() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Name of the Keyfile to process. Must have columns
cultivar, flowcell_lane, filename, and PlateID. Optionally
for paired end reads, filename2 is needed. If filename2
is not supplied, Minimap2 will be setup to run in single
end mode. Otherwise will be paired.
- keyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set keyFile. Name of the Keyfile to process. Must
have columns cultivar, flowcell_lane, filename, and
PlateID. Optionally for paired end reads, filename2
is needed. If filename2 is not supplied, Minimap2
will be setup to run in single end mode. Otherwise
will be paired.
- keyFile() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Name of the Keyfile to process. Must have columns
cultivar, flowcell_lane, filename, and PlateID. Optionally
for paired end reads, filename2 is needed. If filename2
is not supplied, Minimap2 will run in single end mode.
Otherwise will be paired.
- keyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set keyFile. Name of the Keyfile to process. Must
have columns cultivar, flowcell_lane, filename, and
PlateID. Optionally for paired end reads, filename2
is needed. If filename2 is not supplied, Minimap2
will run in single end mode. Otherwise will be paired.
- keyFile() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Name of the Keyfile to process. Must have columns
cultivar, flowcell_lane, filename, and PlateID. Optionally
for paired end reads, filename2 is needed. If filename2
is not supplied, Minimap2 will run in single end mode.
Otherwise will be paired.
- keyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set keyFile. Name of the Keyfile to process. Must
have columns cultivar, flowcell_lane, filename, and
PlateID. Optionally for paired end reads, filename2
is needed. If filename2 is not supplied, Minimap2
will run in single end mode. Otherwise will be paired.
- keyFile() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Name of the Keyfile to process. Must have columns
cultivar, flowcell_lane, filename, and PlateID. In
the filename column a GVCF file needs to be specified
- keyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Set keyFile. Name of the Keyfile to process. Must
have columns cultivar, flowcell_lane, filename, and
PlateID. In the filename column a GVCF file needs to
be specified
- keyFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Name of the Keyfile to process. Must have columns
AssemblyServerDir, AssemblyGenomeFasta, RefDir, RefFasta,
AssemblyDir, AssemblyFasta, AssemblyDBName, and Chromosome.
The AssemblyFasta column should contain the name of
the assembly chromosome fasta file for aligning. The
AssemblyGenomeFasta column should contain the name
of the full genome fasta from which the chromosome
only fasta came.
- keyFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Set keyFile. Name of the Keyfile to process. Must
have columns AssemblyServerDir, AssemblyGenomeFasta,
RefDir, RefFasta, AssemblyDir, AssemblyFasta, AssemblyDBName,
and Chromosome. The AssemblyFasta column should contain
the name of the assembly chromosome fasta file for
aligning. The AssemblyGenomeFasta column should contain
the name of the full genome fasta from which the chromosome
only fasta came.
- keyFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Name of the Keyfile to process. Must have columns
AssemblyServerDir, AssemblyGenomeFasta, RefDir, RefFasta,
AssemblyDir, AssemblyFasta, and AssemblyDBName. The
AssemblyFasta column should contain the name of the
assembly fasta file for aligning. The AssemblyGenomeFasta
column should contain the name of the full genome fasta
from which the assembly fasta came (it may be the same
name as the AssemblyGenomeFasta).
- keyFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Set keyFile. Name of the Keyfile to process. Must
have columns AssemblyServerDir, AssemblyGenomeFasta,
RefDir, RefFasta, AssemblyDir, AssemblyFasta, and AssemblyDBName.
The AssemblyFasta column should contain the name of
the assembly fasta file for aligning. The AssemblyGenomeFasta
column should contain the name of the full genome fasta
from which the assembly fasta came (it may be the same
name as the AssemblyGenomeFasta).
- keyFile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- keyFileDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- KeyFileUniqueRecord - Class in net.maizegenetics.pangenome.hapCalling
-
- KeyFileUniqueRecord(methodName, taxonName, fileGroupName) - Constructor for class net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord
-
- KmerBasedConsensusUtils - Class in net.maizegenetics.pangenome.hapcollapse
-
- kmerDistanceMatrix(referenceRange, nodes, kmerSize, calculationType) - Static method in class net.maizegenetics.pangenome.hapcollapse.KmerBasedConsensusUtils
-
This returns the distance matrix for the taxa in the given reference range using the method of distance calculation
- kmerDistanceMatrix(sequenceMap, kmerSize, calculationType) - Static method in class net.maizegenetics.pangenome.hapcollapse.KmerBasedConsensusUtils
-
This returns a distance matrix for a map of Taxon -> sequence, where sequence is string of nucleotides
- kmerDistFile() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Kmer to Distance files.
- kmerDistFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Set Kmer Dist Export. Kmer to Distance files.
- kmerDNASequence() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- kmerLongSequence() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- KmerMap - Class in net.maizegenetics.pangenome.hapCalling
-
KmerMap provides high efficiency in both speed and memory efficiency for storing and counting kmers.
It is backed with a primitive hashmap.
All kmers are encoded into Longs, so only kmers upto to 32bp in length can be stored.
- KmerMap(sequence, kmerSize, stepSize, kmerPrefix, refRangeId, mapType) - Constructor for class net.maizegenetics.pangenome.hapCalling.KmerMap
-
KmerMap provides high efficiency in both speed and memory efficiency for storing and counting kmers.
It is backed with a primitive hashmap.
All kmers are encoded into Longs, so only kmers upto to 32bp in length can be stored.
- kmerMapFile() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
Text file to store haplotype scoring
- kmerMapFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
Set Kmer Map File. Text file to store haplotype scoring
- kmerMapFile() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Binary file of kmer and haplotype ids
- kmerMapFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Set Kmer Map File. Binary file of kmer and haplotype
ids
- KmerMapType - Enum in net.maizegenetics.pangenome.hapCalling
-
- kmersAsDNA() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- kmersAsLongArray() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- kmersAsLongList() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- kmersAsLongSet() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- kmerSize() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
kmer size for indexing genome
- kmerSize(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
Set Kmer Size. kmer size for indexing genome
- kmerSize() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
kmer size for indexing genome. Maximum size is 32.
Use the default of 32 unless you know what you are
doing.
- kmerSize(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Set Kmer Size. kmer size for indexing genome. Maximum
size is 32. Use the default of 32 unless you know what
you are doing.
- kmerSize() - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
Kmer size
- kmerSize(value) - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
Set Kmer Size. Kmer size
- kmerSize() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
Kmer size
- kmerSize(value) - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
Set Kmer Size. Kmer size
- kmerSize() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Kmer size
- kmerSize(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Kmer Size. Kmer size
- kmerStepSize(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Set Kmer Step Size. kmer step size for the sliding
window when indexing genome. Minimum size is 1. A
higher step size will give you less kmers.
- kmerStepSize() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
kmer step size for the sliding window when indexing
genome. Minimum size is 1. A higher step size will
give you less kmers.
- KmerToRefRangeIdToPurgeArray - Class in net.maizegenetics.pangenome.hapCalling
-
Simple data class to hold the three arrays.
- KmerToRefRangeIdToPurgeArray(kmerArray, refRangeIdArray, purgeArray) - Constructor for class net.maizegenetics.pangenome.hapCalling.KmerToRefRangeIdToPurgeArray
-
Simple data class to hold the three arrays.
- KmerUtils - Class in net.maizegenetics.pangenome.hapCalling
-
- lastReferenceRange() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns the last reference range in this graph.
- lastReferenceRange(chr) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns the last reference range for the given chromosome.
- launchProcessor($receiver, id, channel) - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
Call converter function on each file
- leftEdges(node) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns List of Left HaplotypeEdges for given HaplotypeNode
- leftHapNode() - Method in class net.maizegenetics.pangenome.api.HaplotypeEdge
-
HaplotypeNode to the left of the current edge.
- leftTrimCount() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
-
- length() - Method in class net.maizegenetics.pangenome.api.AlleleInfo
-
- length() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- length() - Method in class net.maizegenetics.pangenome.api.HaplotypeSequence
-
- likelihood() - Method in class net.maizegenetics.pangenome.api.HaplotypePath
-
Likelihood of haplotype path calculated from all included haplotype nodes
- likelyParentFile() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
The name and path of the file of likely parents and
their read counts.
- likelyParentFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Parent Output File. The name and path of the file
of likely parents and their read counts.
- likelyParentFile() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
The name and path of the file of likely parents and
their read counts. If no file name is provided the
likely parents will not be written to a file.
- likelyParentFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Parent Output File. The name and path of the file
of likely parents and their read counts. If no file
name is provided the likely parents will not be written
to a file.
- LikelyParentsPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
This plugin finds the most likely parents for each of a series of read mapppings specified by either a read method
or a key file. The parents are selected in a stepwise manner by finding the parent with the most mapped reads not
mapped to previously selected parents. Additional parents are selected until maxParents have been selected,
all available parents are selected, or minCoverage is reached. minCoverage is calculated as the number of reads
mapping to any of the likely parents divided by the total number of reads.
- LikelyParentsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
This plugin finds the most likely parents for each of a series of read mapppings specified by either a read method
or a key file. The parents are selected in a stepwise manner by finding the parent with the most mapped reads not
mapped to previously selected parents. Additional parents are selected until maxParents have been selected,
all available parents are selected, or minCoverage is reached. minCoverage is calculated as the number of reads
mapping to any of the likely parents divided by the total number of reads.
- LikelyParentsPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
This plugin finds the most likely parents for each of a series of read mapppings specified by either a read method
or a key file. The parents are selected in a stepwise manner by finding the parent with the most mapped reads not
mapped to previously selected parents. Additional parents are selected until maxParents have been selected,
all available parents are selected, or minCoverage is reached. minCoverage is calculated as the number of reads
mapping to any of the likely parents divided by the total number of reads.
- line_data() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
-
- line_name() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
-
- lineName() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
Name name to be stored in the genotypes table, e.g. B73_Assembly
- lineName(value) - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
Set Line Name. Name name to be stored in the genotypes table, e.g. B73_Assembly
- lineName() - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
the name of the line for which reads will be simulated.
If not specified, all lines will be simulated for the
haplotype method.
- lineName(value) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
Set Line Name. the name of the line for which reads
will be simulated. If not specified, all lines will
be simulated for the haplotype method.
- lineToFasta(line, sampleName, counter) - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
Given a string in FASTQCOL format and associated metadata, return a string in fasta format
FASTQCOL is really a csv file with four columns:
- lineToFastq(line, sampleName, counter) - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaConverter
-
Given a string in FASTQCOL format and associated metadata, return a string in fastq format
Parameters:
line: the input string, in FASTQCOL format
sampleName: the name of the original file, minus extensions
counter: the row number of this line in the original file
- LiquibaseCommandPlugin - Class in net.maizegenetics.pangenome.pipeline
-
This class is written specifically to test the PipelineUtils:runLiquibaseCommand() function
Is this the best way to do this? This is called from a docker from within kotlin/test/pipeline/PipelineUtilsTest
- LiquibaseCommandPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPlugin
-
This class is written specifically to test the PipelineUtils:runLiquibaseCommand() function
Is this the best way to do this? This is called from a docker from within kotlin/test/pipeline/PipelineUtilsTest
- LiquibaseCommandPlugin() - Constructor for class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPlugin
-
This class is written specifically to test the PipelineUtils:runLiquibaseCommand() function
Is this the best way to do this? This is called from a docker from within kotlin/test/pipeline/PipelineUtilsTest
- LiquibaseCommandPluginKt - Class in net.maizegenetics.pangenome.pipeline
-
- liquibaseOutputDir() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
The directory to which liquibase output files will
be written.
- liquibaseOutputDir(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Liquibase Outdir. The directory to which liquibase
output files will be written.
- liquibaseOutputDir() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
The directory to which liquibase output files will
be written.
- liquibaseOutputDir(value) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Set Liquibase Outdir. The directory to which liquibase
output files will be written.
- LiquibaseUpdatePlugin - Class in net.maizegenetics.pangenome.liquibase
-
This script is the second of a pair. When called from the RunLiquibaseUPdates.sh, it follows
a call to CheckDBVersionPlugin. The latter verifies the db is a candidate for liquibase
updates (ie, it contains tables/columns indicating the version is appropriate for the
current liquibase changesets).
- LiquibaseUpdatePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin
-
This script is the second of a pair. When called from the RunLiquibaseUPdates.sh, it follows
a call to CheckDBVersionPlugin. The latter verifies the db is a candidate for liquibase
updates (ie, it contains tables/columns indicating the version is appropriate for the
current liquibase changesets).
- LiquibaseUpdatePluginKt - Class in net.maizegenetics.pangenome.liquibase
-
- listTaxa() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
Writes the names of the taxa in the HaplotypeGraph, myGraph, to System.out
- lnTransitionProbability(from, to) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbabilityWithInbreeding
-
- LoadAllIntervalsToPHGdbPlugin - Class in net.maizegenetics.pangenome.db_loading
-
This class takes as input a BED formatted intervals file. Expected BED header columns are "chrom", "chromStart", "chromEnd",
and "name" (as per the bed file format requirements. Any other columns in the bed file are ignored.
- LoadAllIntervalsToPHGdbPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
This class takes as input a BED formatted intervals file. Expected BED header columns are "chrom", "chromStart", "chromEnd",
and "name" (as per the bed file format requirements. Any other columns in the bed file are ignored.
- LoadAllIntervalsToPHGdbPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
This class takes as input a BED formatted intervals file. Expected BED header columns are "chrom", "chromStart", "chromEnd",
and "name" (as per the bed file format requirements. Any other columns in the bed file are ignored.
- LoadAllIntervalsToPHGdbPluginKt - Class in net.maizegenetics.pangenome.db_loading
-
- loadASMHaplotypes(gvcfKeyFile) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
function to load assembly haplotypes from GVCF files via LoadHaplotypesFromGVCFPlugin.
- loadAssemblyDataToDB(gamete_grp_id, method, dbConn, anchorSequences, chromosome, genomeFileId) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Load the assembly haplotype data to the database
- loadConda() - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
Load dependencies from conda
- loadConda(value) - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
Set Load From Conda. Load dependencies from conda
- loadDB() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Boolean: true means load haplotypes to db, false means
do not populate the database. Defaults to true
- loadDB(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Set Load to DataBase. Boolean: true means load haplotypes
to db, false means do not populate the database. Defaults
to true
- loadDBDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- loadDBDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- loadFromDB() - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Load from multiple DBs if this is set to true. If
false, we will treat the files in the directory to
be raw flat files
- loadFromDB(value) - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Set Load From D B. Load from multiple DBs if this is
set to true. If false, we will treat the files in
the directory to be raw flat files
- loadGFFsToGff3Feature(keyFile) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Function takes a key file with columns taxon, gffFile.
For each taxon, read the gff file using htsjdk gff feature reader.
Return a map of taxon to associated Gff3Feature entries
- LoadHaplotypesFromGVCFPlugin - Class in net.maizegenetics.pangenome.db_loading
-
Plugin to load up a list of GVCF files given an input keyfile.
- LoadHaplotypesFromGVCFPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Plugin to load up a list of GVCF files given an input keyfile.
- LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord - Class in net.maizegenetics.pangenome.db_loading
-
- LoadHaplotypesFromGVCFPluginKt - Class in net.maizegenetics.pangenome.db_loading
-
- loadInitialAssemblyData(assemblyName, method, clusterSize, dbConn, pluginParams, fastaInfo, isTestMethod) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
load initial genotype and method data to the database
- loadInMAFFile(mafFile) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MafUtils
-
Function to load in the MAF file.
This MAF file will need to only have 2 samples. The first is assumed to be the Reference and the second is the Assembly.
Any extra will be ignored.
This will also skip over any e or i lines.
- loadInReadMappingKeyFile(keyFileName, inputFileFormat, inputFileDir, methodName) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
- loadInWiggleFiles(coverageDir) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function to load in the Wiggle Files in a directory. This works with both Coverage and Identity files.
- loadReadMappingsToDB(hapIdMapping, taxon, fileGroupName, pluginParams, methodDescription, phg, methodName, keyFileRecordsToMappingId, keyFileRecord, outputDebugReadMappingDir, isTestMethod, hapListId, hapIdToRefRangeMap, refRangeToHapIdMap) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to load the Read Mappings to the DB. This will encode the ReadMappings and the load them in given the provided information.
- loadSAMFileIntoSAMReader(fileName) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to load the SAM file into a SAM reader
Could remove this, but we should leave it in as you may need to read from a file in the future.
- localConsensusDirectoryOut - Static variable in class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
-
- localDirectory - Static variable in class net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
-
- localDirectory - Static variable in class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
-
- localDirectory - Static variable in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
-
- localDirectoryOut - Static variable in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
-
- localGvcfDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- localGvcfDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- localGVCFFolder() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Local folder to which gvcf file will be downloaded.
- localGVCFFolder(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Set local gvcf folder path
- localGVCFFolder() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
Local folder to which gvcf file will be downloaded.
- localGVCFFolder(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
Set local gvcf folder path
- localGVCFFolder() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Folder where gvcfs will be downloaded and stored
- localGVCFFolder(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Local GVCF Folder. Folder where gvcfs will be downloaded
and stored
- localGVCFFolder() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Folder where ref and assembly gvcfs are stored. If
non-null, the ref and assembly gvcfs will be copied
to the indicated local download folder for use when
creating consensus haplotypes.
- localGVCFFolder(value) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Set Local GVCF Folder. Folder where ref and assembly
gvcfs are stored. If non-null, the ref and assembly
gvcfs will be copied to the indicated local download
folder for use when creating consensus haplotypes.
- logFactorial(intval) - Static method in class net.maizegenetics.pangenome.hapCalling.FindBestDiploidPathKt
-
Calculates the log factorial of any positive integer using the exact value for 0 to 10 and
Stirlings approximation for integers greater than 10. The formula is taken from the
Wikipedia article for Stirlings approximation
- loggingFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
-
- loggingFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
-
- loggingFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
-
- longestIncreasingSubsequenceLAGAN(pairedSimilarFragments) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.SyntenicAnchors
-
- longListToByteArray(ListOfLongs) - Static method in class net.maizegenetics.pangenome.db_loading.VariantsProcessingUtils
-
- longToIntArray(myLong) - Static method in class net.maizegenetics.pangenome.hapCalling.FindBestDiploidPathKt
-
- lowerPoissonBound() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
Lower Poisson Bound used for filtering.
- lowerPoissonBound(value) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
Set Lower Poisson Bound. Lower Poisson Bound used for filtering.
- lowMemMode() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Run in low memory mode.
- lowMemMode(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Low Mem Mode. Run in low memory mode.
- lowMemMode() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Run in low memory mode.
- lowMemMode(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set Low Mem Mode. Run in low memory mode.
- mAFFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Input MAF file
- mAFFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Set Maf File. Input MAF file
- MAFRecord(score, refRecord, altRecord) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.MAFRecord
-
- MAFToGVCFPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This plugin will take in a MAF file and will output a GVCF file for use in the PHG.
It will keep track of SNP, indel and Ref positions and will also keep track of the ASM chrom, start, end and strand positions.
- MAFToGVCFPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
This plugin will take in a MAF file and will output a GVCF file for use in the PHG.
It will keep track of SNP, indel and Ref positions and will also keep track of the ASM chrom, start, end and strand positions.
- MAFToGVCFPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
This plugin will take in a MAF file and will output a GVCF file for use in the PHG.
It will keep track of SNP, indel and Ref positions and will also keep track of the ASM chrom, start, end and strand positions.
- MAFToGVCFPlugin.AlignmentBlock - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- MAFToGVCFPlugin.AssemblyVariantInfo - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- MAFToGVCFPlugin.MAFRecord - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- MAFToGVCFPlugin.OUTPUT_TYPE - Enum in net.maizegenetics.pangenome.processAssemblyGenomes
-
- MAFToGVCFPluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- MafUtils - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- MafUtilsKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- main(args) - Static method in class net.maizegenetics.pangenome.annotations.PathToGFFPluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.api.AddPathsToGraphPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
- main(args) - Static method in class net.maizegenetics.pangenome.CompareFastaToReference
-
- main(args) - Static method in class net.maizegenetics.pangenome.CompareHaplotypesToAssembly
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.ChangeDBMethodTypePluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.CreateBiggerIntervals
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.CreateCSV_TrimmedAnchorLoading
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFile
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
-
Deprecated.
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.FindTrimmedAnchorCoordinates
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.FindTrimmedAssemblyCoordinates
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.ShellScript_createLoadHaplotypes
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.db_updateDelete.DeleteReadMappingPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.fastaExtraction.CreateDBLoadScripts
-
- main(args) - Static method in class net.maizegenetics.pangenome.fastaExtraction.CreateFastaDBFiles
-
- main(args) - Static method in class net.maizegenetics.pangenome.fastaExtraction.ExtractFastaFromGVCFCBSU
-
- main(args) - Static method in class net.maizegenetics.pangenome.GenerateHaplotypeCallerScripts
-
- main(args) - Static method in class net.maizegenetics.pangenome.GetFastaSequenceLengths
-
- main(args) - Static method in class net.maizegenetics.pangenome.GVCFStats
-
- main() - Static method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapcollapse.CompareAssembliesToReference
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapcollapse.CreateHaplotypesFromFasta
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
- main() - Static method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapcollapse.PurgeSequencesFromAlignments
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
-
- main() - Static method in class net.maizegenetics.pangenome.hapcollapse.RankingFilePluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.hapcollapse.RunGVCFTyper
-
- main(args) - Static method in class net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
-
- main(args) - Static method in class net.maizegenetics.pangenome.multiSequenceAlignment.RemoveLongRunNs
-
- main(args) - Static method in class net.maizegenetics.pangenome.multiSequenceAlignment.SplitMafftRun
-
- main(args) - Static method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.pipeline.MakeDefaultDirectoryPluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.pipeline.MakeInitialPHGDBPipelinePluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
-
- main(args) - Static method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
- main(args) - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
-
- main(args) - Static method in class net.maizegenetics.pangenome.pipelineTests.GenerateRForPHG
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MafUtilsKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- main(args) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
- main() - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPluginKt
-
- main() - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPluginKt
-
- main(args) - Static method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
- main(args) - Static method in class net.maizegenetics.pangenome.Utils.CreateHashForFiles
-
- mainProcessDataJustGenes(geneFile, outputBase, chr) - Static method in class net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF
-
- mainProcessMergeOverlapsAddGapDifference(geneFile, outputBase, chr, numFlanking) - Static method in class net.maizegenetics.pangenome.db_loading.CreateAnchorFilesFromGeneGFF
-
- makeBAMDir() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Make the BAM Directory by adding a mkdir command to
the script.
- makeBAMDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set Make BAM Directory. Make the BAM Directory by adding
a mkdir command to the script.
- MakeDefaultDirectoryPlugin - Class in net.maizegenetics.pangenome.pipeline
-
- MakeDefaultDirectoryPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.pipeline.MakeDefaultDirectoryPlugin
-
- MakeDefaultDirectoryPlugin() - Constructor for class net.maizegenetics.pangenome.pipeline.MakeDefaultDirectoryPlugin
-
- MakeDefaultDirectoryPluginKt - Class in net.maizegenetics.pangenome.pipeline
-
- makeDiploid() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
Whether to report haploid paths as homozygousdiploid
- makeDiploid(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
Set Make Diploid. Whether to report haploid paths as homozygousdiploid
- makeDiploid() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Whether to report haploid paths as homozygousdiploid
- makeDiploid(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Set Make Diploid. Whether to report haploid paths as homozygousdiploid
- makeGffFromPath(path, centerGffs, graph, outputFile) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
This method takes a path ( a list of integer haplotype ids),
a phg graph that is based on the haplotypeIds in the path,
and an optional output file name.
- MakeInitialPHGDBPipelinePlugin - Class in net.maizegenetics.pangenome.pipeline
-
This class runs the loadALlIntervalsToPHGdbPlugin to create and populate with reference ranges
and initial PHG databse.
- MakeInitialPHGDBPipelinePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.pipeline.MakeInitialPHGDBPipelinePlugin
-
This class runs the loadALlIntervalsToPHGdbPlugin to create and populate with reference ranges
and initial PHG databse.
- MakeInitialPHGDBPipelinePlugin() - Constructor for class net.maizegenetics.pangenome.pipeline.MakeInitialPHGDBPipelinePlugin
-
This class runs the loadALlIntervalsToPHGdbPlugin to create and populate with reference ranges
and initial PHG databse.
- MakeInitialPHGDBPipelinePluginKt - Class in net.maizegenetics.pangenome.pipeline
-
- mappingFileDir() - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Name of the haplotype count file.
- mappingFileDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Set Output Read Mapping file Dir. Name of the haplotype
count file.
- mappingStatDir() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Directory to store the mapping stats.
- mappingStatDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Output Secondary Mapping Stat Directory. Directory
to store the mapping stats.
- markKmersForPurgeUsingHammingDistance(kmerToRefRange, kmerSize, minAllowedHammingDist, verboseLogging) - Static method in class net.maizegenetics.pangenome.hapCalling.KmerUtils
-
Method that will mark Kmers to purge using HammingDistance
- matrix - Variable in class net.maizegenetics.pangenome.api.RMethods.MatrixWithNames
-
- maxClusters() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
When attempting to subdivide genic ranges, only genic
ranges with more than maxClusters haplotypes after
clustering will be subdivided.
- maxClusters(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Max Clusters. When attempting to subdivide genic
ranges, only genic ranges with more than maxClusters
haplotypes after clustering will be subdivided.
- maxDBUploadQueue() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Number of Haplotype instances to stage per chromosome
before a DB write is triggered. Lower this number
if you are running into RAM issues. It will take longer
to process, but should help balance the load.
- maxDBUploadQueue(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Set Max Num Haps Staged. Number of Haplotype instances
to stage per chromosome before a DB write is triggered.
Lower this number if you are running into RAM issues.
It will take longer to process, but should help balance
the load.
- maxDistance(matrix, row, col) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
Function to figure out what the maximum row and col distance are for a given position in the oringinal distance Matrix.
- maxDistFromFounder() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Maximum genetic divergence from founder haplotype to cluster sequences
- maxDistFromFounder(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Max divergence from founder. Maximum genetic divergence from founder haplotype to cluster sequences
- maxDiversity() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
This parameter determines the maximum diversity allowed
in the clustering step used to determine haplotype
number. Haplotype number is used to decide when to
split genic ranges.
- maxDiversity(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Mx Div. This parameter determines the maximum diversity
allowed in the clustering step used to determine haplotype
number. Haplotype number is used to decide when to
split genic ranges.
- maxError - Static variable in class net.maizegenetics.pangenome.api.VariantUtils
-
- maxError() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Maximum error allowed to create a homozygous call. If the error rate is above this value N or Major allele will be exported for that site
- maxError(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Maximum error. Maximum error allowed to create a homozygous call. If the error rate is above this value N or Major allele will be exported for that site
- maxIndexAndProbabilityForTarget(fromProbability, to) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbabilityWithInbreeding
-
Adds the vector of
fromProbability to a vector of transition probabilities and returns
the index of the maximum value and the maximum value as a Pair
- maxKmerCountPerRefRange() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Maximum kmer counts to be included in processing.
This is to reduce the number of highly repetative kmers
- maxKmerCountPerRefRange(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Set Max Kmer Count Per Range. Maximum kmer counts to
be included in processing. This is to reduce the number
of highly repetative kmers
- maxNan() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Maximum proportion of Nans allowed in a row of the relationship matrix
- maxNan(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Max Nan. Maximum proportion of Nans allowed in a row of the relationship matrix
- maxNodesPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
maximum number of nodes per reference range. Ranges
with more nodes will not be included in the output
node list.
- maxNodesPerRange(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Max Nodes. maximum number of nodes per reference
range. Ranges with more nodes will not be included
in the output node list.
- maxNodesPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Any range with more than maxHap haplotypes will not
be included in the path.
- maxNodesPerRange(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Maximum Number of Haplotypes. Any range with more
than maxHap haplotypes will not be included in the
path.
- maxNodesPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
maximum number of nodes per reference range. Ranges with more nodes will not be included in the output node list.
- maxNodesPerRange(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Max Nodes. maximum number of nodes per reference range. Ranges with more nodes will not be included in the output node list.
- maxNumberOfClusters() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
The maximum number of clusters allowed. This value overrides mxDiv if it results in more clusters.
- maxNumberOfClusters(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Max Clust. The maximum number of clusters allowed. This value overrides mxDiv if it results in more clusters.
- maxNumberOfClusters() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
The maximum number of clusters that will be created for a reference range. If mxDiv produces too many clusters then the cut height that produces maxClusters number of clusters will be substituted.
- maxNumberOfClusters(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Maximum Cluster Number. The maximum number of clusters that will be created for a reference range. If mxDiv produces too many clusters then the cut height that produces maxClusters number of clusters will be substituted.
- maxNumberOfParents() - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
The maximum number of parents to be selected.
- maxNumberOfParents(value) - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
Set Max Parents. The maximum number of parents to be
selected.
- maxParents() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
To restrict path finding to the most likely parents,
the number of parents used will not be greater than
maxParents. The number of parents used will be the
minimum of maxParents and the number of parents needed
to reach minCoverage. If both maxParents and minCoverage
are left at the default, all parents in the input HaplotypeGraph
will be used.
- maxParents(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Max Parents. To restrict path finding to the most
likely parents, the number of parents used will not
be greater than maxParents. The number of parents used
will be the minimum of maxParents and the number of
parents needed to reach minCoverage. If both maxParents
and minCoverage are left at the default, all parents
in the input HaplotypeGraph will be used.
- maxParents() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
To restrict path finding to the most likely parents,
the number of parents used will not be greater than
maxParents. The number of parents used will be the
minimum of maxParents and the number of parents needed
to reach minCoverage. If both maxParents and minCoverage
are left at the default, all parents in the input HaplotypeGraph
will be used.
- maxParents(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Max Parents. To restrict path finding to the most
likely parents, the number of parents used will not
be greater than maxParents. The number of parents used
will be the minimum of maxParents and the number of
parents needed to reach minCoverage. If both maxParents
and minCoverage are left at the default, all parents
in the input HaplotypeGraph will be used.
- maxReadsPerKB() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
maximum number of include counts per anchor reference
range Kb. Ranges with more reads will not be included
in the output node list.
- maxReadsPerKB(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Max Reads. maximum number of include counts per
anchor reference range Kb. Ranges with more reads will
not be included in the output node list.
- maxReadsPerKB() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Any range with more than maxReadsKB reads per kilobase
of sequence will not be included in the path.
- maxReadsPerKB(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Maximum Reads per KB. Any range with more than
maxReadsKB reads per kilobase of sequence will not
be included in the path.
- maxReadsPerKB() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
maximum number of include counts per anchor reference range. Ranges with more reads will not be included in the output node list.
- maxReadsPerKB(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Max Reads. maximum number of include counts per anchor reference range. Ranges with more reads will not be included in the output node list.
- maxReadsPerRangeKB(maxReads) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- maxRefRangeError() - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Maximum allowed error when choosing best reference
range to count. Error is computed 1 - (mostHitRefCount/totalHits)
- maxRefRangeError(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Set Max Ref Rage Err. Maximum allowed error when choosing
best reference range to count. Error is computed 1
- maxRefRangeError() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
Maximum allowed error when choosing best reference
range to count. Error is computed 1 - (mostHitRefCount/totalHits)
- maxRefRangeError(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
Set Max Ref Rage Err. Maximum allowed error when choosing
best reference range to count. Error is computed 1
- maxRefRangeError() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Maximum allowed error when choosing best reference
range to count. Error is computed 1 - (mostHitRefCount/totalHits)
- maxRefRangeError(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Max Ref Range Err. Maximum allowed error when choosing
best reference range to count. Error is computed 1
- maxRefRangeError() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Maximum allowed error when choosing best reference
range to count. Error is computed 1 - (mostHitRefCount/totalHits)
- maxRefRangeError(value) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Set Max Ref Range Err. Maximum allowed error when choosing
best reference range to count. Error is computed 1
- maxRefRangeError() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Maximum allowed error when choosing best reference
range to count. Error is computed 1 - (mostHitRefCount/totalHits)
- maxRefRangeError(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Max Ref Range Err. Maximum allowed error when choosing
best reference range to count. Error is computed 1
- maxRefRangeError() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Maximum allowed error when choosing best reference
range to count. Error is computed 1 - (mostHitRefCount/totalHits)
- maxRefRangeError(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set Max Ref Range Err. Maximum allowed error when choosing
best reference range to count. Error is computed 1
- maxSearchWindow() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
The number of bps when checking coverage to walk out.
- maxSearchWindow(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Maximum Search Window. The number of bps when checking
coverage to walk out.
- maxSecondaryAlignments() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Maximum number of secondary alignments to be returned
by minimap2. This will be the value of the -N parameter
in the minimap2 command line. If the value is too low,
some valid read mappings will not be reported.
- maxSecondaryAlignments(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Max Secondary. Maximum number of secondary alignments
to be returned by minimap2. This will be the value
of the -N parameter in the minimap2 command line. If
the value is too low, some valid read mappings will
not be reported.
- maxThreads() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
The maximum number of threads to be used to create consensi. The actual number of threads used will not be greater than number of available CPU's - 2.
- maxThreads(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Max Threads. The maximum number of threads to be used to create consensi. The actual number of threads used will not be greater than number of available CPU's - 2.
- memoryUse() - Static method in class net.maizegenetics.pangenome.hapCalling.FindBestDiploidPathKt
-
- mergeCoords(coordFile, chromosome) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Deprecated.
- MergeFastqPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Plugin to combine all fastq files in the input -fastqDir into sets of combined Fastqs.
he number to be batched together is set by -numToMerge. It will also generate a template script for running minimap2
If -useOriginalReadNames is set to true, the fastq records will not be renamed.
This should only be used if the read names are unique in each fastq. Otherwise minimap2 will mix samples.
- MergeFastqPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Plugin to combine all fastq files in the input -fastqDir into sets of combined Fastqs.
he number to be batched together is set by -numToMerge. It will also generate a template script for running minimap2
If -useOriginalReadNames is set to true, the fastq records will not be renamed.
This should only be used if the read names are unique in each fastq. Otherwise minimap2 will mix samples.
- MergeFastqPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Plugin to combine all fastq files in the input -fastqDir into sets of combined Fastqs.
he number to be batched together is set by -numToMerge. It will also generate a template script for running minimap2
If -useOriginalReadNames is set to true, the fastq records will not be renamed.
This should only be used if the read names are unique in each fastq. Otherwise minimap2 will mix samples.
- MergeFastqPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- mergeFiles(mergedFileName, outputGroupingWriter, fileList, batchId) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
- mergeGenicRegions(genicRegions) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Simple function to merge the genic regions together if they overlap bps.
- MergeGVCFPlugin - Class in net.maizegenetics.pangenome.hapcollapse
-
Deprecated.
- MergeGVCFPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
-
Deprecated.
- MergeGVCFUtils - Class in net.maizegenetics.pangenome.hapcollapse
-
Deprecated.
- mergeOverlaps() - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
Whether to merge any overlapping ranges found in the
bed file. Default is no. If overlaps are found and
mergeOverLaps is no, processing will be stopped and
error printed.
- mergeOverlaps(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
Set Merge Overlapping Ranges. Whether to merge any
overlapping ranges found in the bed file. Default
is no. If overlaps are found and mergeOverLaps is
no, processing will be stopped and error printed.
- mergeRefBlocks(refBlocks, refRangeStart, refRangeEnd) - Static method in class net.maizegenetics.pangenome.api.MergeVariantInfosKt
-
Function to merge the reference blocks
- mergeRefBlocks() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Merge consecutive GVCF ReferenceBlocks together. If
there is at least 1 bp between two gvcf refBlock records,
the records will not be merged
- mergeRefBlocks(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Set Merge Ref Blocks. Merge consecutive GVCF ReferenceBlocks
together. If there is at least 1 bp between two gvcf
refBlock records, the records will not be merged
- mergeRule() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
The rule in which to resolve the conflicting Indels after consensus has been found.
- mergeRule(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Set Indel Merge Rule. The rule in which to resolve the conflicting Indels after consensus has been found.
- mergeUsingKeyFile(fastqDirectory, inputKeyFile) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
- MergeVariantInfosKt - Class in net.maizegenetics.pangenome.api
-
- method() - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
Path method name If present, only
taxa from the taxa input that were stored with this
method will have their paths pulled from the db.
- method(value) - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
Set Method
If present, only taxa from the taxa input that were
stored with this method will have their paths pulled
from the db.
- Method - Class in net.maizegenetics.pangenome.api
-
Data class for holding row from the PHG methods table.
- Method(name, id, type) - Constructor for class net.maizegenetics.pangenome.api.Method
-
Data class for holding row from the PHG methods table.
- method(emissionMethod) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
-
- method() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Method name for the haplotypes being uploaded.
- method(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Set Method. Method name for the haplotypes being uploaded.
- methodDescription() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Method description to be written if the method is new.
- methodDescription(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Set Method Description. Method description to be written
if the method is new.
- methodDescription() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Method description to be stored in the DB.
- methodDescription(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Method Description. Method description to be stored
in the DB.
- methodDescription() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Method description to be stored in the DB.
- methodDescription(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Method Description. Method description to be stored
in the DB.
- methodDescription() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Method description to be stored in the DB.
- methodDescription(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set Method Description. Method description to be stored
in the DB.
- methodDescription() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Method description to be stored in the DB.
- methodDescription(value) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Set Method Description. Method description to be stored
in the DB.
- methodDetails() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
Desscription for this group of reference ranges.
- methodDetails(value) - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
Set Method Details. Desscription for this group of reference ranges.
- methodId(database, method_name) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Returns method id (methods.method_id) for given method name.
- methodIds - Variable in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataVectors
-
- methodName() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
Method name for this reference range group.
- methodName(value) - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
Set Method Name. Method name for this reference range group.
- methodName() - Method in class net.maizegenetics.pangenome.db_loading.ChangeDBMethodTypePlugin
-
Name of stored method whose type you would like to
change
- methodName(value) - Method in class net.maizegenetics.pangenome.db_loading.ChangeDBMethodTypePlugin
-
Set Method Name. Name of stored method whose type you
would like to change
- methodName() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPlugin
-
Method name assigned to read mappings that will be
deleted.
- methodName(value) - Method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPlugin
-
Set Method Name. Method name assigned to read mappings
that will be deleted.
- methodName() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeleteReadMappingPlugin
-
Method name assigned to read mappings that will be
deleted.
- methodName(value) - Method in class net.maizegenetics.pangenome.db_updateDelete.DeleteReadMappingPlugin
-
Set Method Name. Method name assigned to read mappings
that will be deleted.
- methodName() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Method name to be stored in the DB.
- methodName(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Method Name. Method name to be stored in the DB.
- methodName() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Method name to be stored in the DB.
- methodName(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Method Name. Method name to be stored in the DB.
- methodName() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Method name to be stored in the DB.
- methodName(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set Method Name. Method name to be stored in the DB.
- methodName() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Method name to be stored in the DB.
- methodName(value) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Set Method Name. Method name to be stored in the DB.
- methods() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,;,;
- methods(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Set Methods. Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,;,;
- methods(database) - Static method in class net.maizegenetics.pangenome.api.HaplotypeGraphStream
-
This loads the contents of the PHG methods table into memory.
- methods() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
Pairs of methods (haplotype method name and range group
method name). Method pair separated by a comma, and
pairs separated by semicolon. The range group is optional
- methods(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
Set Methods. Pairs of methods (haplotype method name
and range group method name). Method pair separated
by a comma, and pairs separated by semicolon. The range
group is optional
Usage: ,;,;
- methods() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,;,;
- methods(value) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
Set Methods. Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,;,;
- methods() - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs
separated by semicolon. The range group is optional
- methods(value) - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
Set Methods. Pairs of methods (haplotype method name and range group method name). Method pair separated by a
comma, and pairs separated by semicolon. The range group is optional Usage: ,;,;
- methods() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Pairs of methods (haplotype method name and range group
method name). Method pair separated by a comma, and
pairs separated by colon. The range group is optional
- methods(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Set Methods. Pairs of methods (haplotype method name
and range group method name). Method pair separated
by a comma, and pairs separated by colon. The range
group is optional
Usage: ,:,:
- methods() - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
Pairs of methods (haplotype method name and range group
method name). Method pair separated by a comma, and
pairs separated by semicolon. The range group is optional
- methods(value) - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
Set Methods. Pairs of methods (haplotype method name
and range group method name). Method pair separated
by a comma, and pairs separated by semicolon. The range
group is optional
Usage: ,;,;
- methods() - Method in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
-
Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,;,;
- methods(value) - Method in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
-
Set Methods. Pairs of methods (haplotype method name and range group method name). Method pair separated by a comma, and pairs separated by semicolon. The range group is optional Usage: ,;,;
- methods() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
Commas separated list of mathod names
- methods(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
Set Methods. Commas separated list of mathod names
- methods() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
Commas separated list of mathod names
- methods(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
Set Methods. Commas separated list of mathod names
- MethodTableReportPlugin - Class in net.maizegenetics.pangenome.api
-
MethodTableReportPlugin exports the contents of the PHG db method table to a table report. Because a number of plugins require method names as parameters, the table contents make a useful reference.
- MethodTableReportPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.api.MethodTableReportPlugin
-
- MethodTableReportPlugin() - Constructor for class net.maizegenetics.pangenome.api.MethodTableReportPlugin
-
- methodType() - Method in class net.maizegenetics.pangenome.db_loading.ChangeDBMethodTypePlugin
-
Integer value of the db method type to be associated
with the supplied method name
- methodType(value) - Method in class net.maizegenetics.pangenome.db_loading.ChangeDBMethodTypePlugin
-
Set PHG Method Type ID. Integer value of the db method
type to be associated with the supplied method name
- minAlleleFrequency() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
At each position, if no allele has the minimum frequency, the consensus haplotype allele will be set to misssing.
- minAlleleFrequency(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Minimum Allele Frequency. At each position, if no allele has the minimum frequency, the consensus haplotype allele will be set to misssing.
- minAllowedHamming() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Minimum kmer count required to define a kmer as unique.
Within reference range, this filter criteria is not
applied. Only when comparing kmers across reference
ranges is Hamming Distance taken into account. A higher
number here should result in fewer kmers as more will
be marked as repetitive.
- minAllowedHamming(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Set Min Allowed Hamming. Minimum kmer count required
to define a kmer as unique. Within reference range,
this filter criteria is not applied. Only when comparing
kmers across reference ranges is Hamming Distance taken
into account. A higher number here should result in
fewer kmers as more will be marked as repetitive.
- minCountTaxa() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
Minimun number of taxa represented in reference range for reference range to remain in graph
- minCountTaxa(value) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
Set Min Count Taxa. Minimun number of taxa represented in reference range for reference range to remain in graph
- minCoverage() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
To restrict path finding to the most likely parents,
the smallest number of parents needed to provide read
coverage greater than or equal to minCoverage will
be used to find paths. If maxParents is smaller, that
number of parents will be used.
- minCoverage(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Min Coverage. To restrict path finding to the most
likely parents, the smallest number of parents needed
to provide read coverage greater than or equal to minCoverage
will be used to find paths. If maxParents is smaller,
that number of parents will be used.
- minCoverage() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
To restrict path finding to the most likely parents,
the smallest number of parents needed to provide read
coverage greater than or equal to minCoverage will
be used to find paths. If maxParents is smaller, that
number of parents will be used.
- minCoverage(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Min Coverage. To restrict path finding to the most
likely parents, the smallest number of parents needed
to provide read coverage greater than or equal to minCoverage
will be used to find paths. If maxParents is smaller,
that number of parents will be used.
- minCoverage() - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
No more parents will be selected when the proportion
of total reads mapped to the selected parents is greater
than or equal to this number.
- minCoverage(value) - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
Set Min Coverage. No more parents will be selected
when the proportion of total reads mapped to the selected
parents is greater than or equal to this number.
- minCoverage() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
The minimum allowed Coverage count for determining
if a bp is conserved or not.
- minCoverage(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Minimum Coverage Count. The minimum allowed Coverage
count for determining if a bp is conserved or not.
- minGenicLength() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
When attempting to subdivide genic ranges, the smallest
allowable subdivision length is minLength base pairs.
- minGenicLength(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Min Length. When attempting to subdivide genic
ranges, the smallest allowable subdivision length is
minLength base pairs.
- minimap2Location() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Location of Minimap2 on file system. This defaults
to use minimap2 if it is on the PATH environment variable.
- minimap2Location(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Set Location of Minimap2 Executable. Location of Minimap2
on file system. This defaults to use minimap2 if it
is on the PATH environment variable.
- Minimap2Utils - Class in net.maizegenetics.pangenome.hapCalling
-
- minimapFParam() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set this to change the -f parameter in minimap2
- minimapFParam(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set Minimap -f Parameter. Set this to change the -f
parameter in minimap2
- minimapLocation() - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Location of Minimap2 on file system. Can use minimap2
if it is on the PATH environment variable. This will
default to minimap2/minimap2 by default.
- minimapLocation(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Set Location of Minimap2 Executable. Location of Minimap2
on file system. Can use minimap2 if it is on the PATH
environment variable. This will default to minimap2/minimap2
by default.
- minimapLocation() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Location of Minimap2 on file system. This defaults
to use minimap2 if it is on the PATH environment variable.
- minimapLocation(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Location of Minimap2 Executable. Location of Minimap2
on file system. This defaults to use minimap2 if it
is on the PATH environment variable.
- minimapLocation() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Location of Minimap2 on file system. This defaults
to use minimap2 if it is on the PATH environment variable.
- minimapLocation(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set Location of Minimap2 Executable. Location of Minimap2
on file system. This defaults to use minimap2 if it
is on the PATH environment variable.
- minimapLocation() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Location of Minimap2 on file system. This defaults
to use minimap2 if it is on the PATH environment variable.
- minimapLocation(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Location of Minimap2 Executable. Location of Minimap2
on file system. This defaults to use minimap2 if it
is on the PATH environment variable.
- minimapNParam() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set this to increase the N parameter used in Minimap2
- minimapNParam(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set Minimap -N parameter. Set this to increase the
N parameter used in Minimap2
- minInversionLen() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Minimum length of inversion for it to be kept as part
of the alignment. Default is 7500
- minInversionLen(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Set Minimum Inversion Length. Minimum length of inversion
for it to be kept as part of the alignment. Default
is 7500
- minInversionLen() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Minimum length of inversion for it to be kept as part of the alignment. Default is 7500.
- minInversionLen(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Set Minimum Inversion Length. Minimum length of inversion for it to be kept as part of the alignment. Default is 7500
- minKmerCountPerRefRange() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Minimum kmer counts to be included in processing.
This is to reduce the number of one off kmers
- minKmerCountPerRefRange(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Set Min Kmer Count Per Range. Minimum kmer counts to
be included in processing. This is to reduce the number
of one off kmers
- minPercentTaxa() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
Minimum percent of taxa represented in reference range for reference range to remain in graph.
- minPercentTaxa(value) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
Set Min Percent Taxa. Minimum percent of taxa represented in reference range for reference range to remain in graph.
- minProbBF() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Only nodes with minP or greater probability will be
kept in the path when using the Backward-Forward algorithm,
- minProbBF(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Min P. Only nodes with minP or greater probability
will be kept in the path when using the Backward-Forward
algorithm,
- minProbBF() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,
- minProbBF(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Min P. Only nodes with minP or greater probability will be kept in the path when using the Backward-Forward algorithm,
- minReads() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
minimum number of reads per anchor reference range.
Ranges with fewer reads will not be included in the
output node list.
- minReads(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Min Reads. minimum number of reads per anchor reference
range. Ranges with fewer reads will not be included
in the output node list.
- minReads() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
- minReads(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Min Reads. minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
- minReadsPerRange(minReads) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- minReadsPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Any range with fewer than minReads will not be included
in the path.
- minReadsPerRange(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Minimum Read Number. Any range with fewer than
minReads will not be included in the path.
- minSiteForComp() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
The minimum number of sites present in two taxa to compare genetic distance to evaluate similarity for clustering
- minSiteForComp(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Min sites to cluster. The minimum number of sites present in two taxa to compare genetic distance to evaluate similarity for clustering
- minSiteForComp() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
The minimum number of shared sites that can be used to calculate the distance between two taxa
- minSiteForComp(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Minimum Sites with Data . The minimum number of shared sites that can be used to calculate the distance between two taxa
- minTaxa() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Minimum number of taxa
- minTaxa(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Min Taxa. Minimum number of taxa
- minTaxaCoverage() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
The minimum proportion of sites present in a taxa to go into clustering
- minTaxaCoverage(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Min taxa coverage. The minimum proportion of sites present in a taxa to go into clustering
- minTaxaCoverage() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Minimum Coverage
- minTaxaCoverage(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Minimum Coverage. Minimum Coverage
- minTaxaInGroup() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Minimum number of taxa to generate a haplotype
- minTaxaInGroup(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Min taxa to generate a haplotype. Minimum number of taxa to generate a haplotype
- minTaxaPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
minimum number of taxa per anchor reference range.
Ranges with fewer taxa will not be included in the
output node list.
- minTaxaPerRange(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Min Taxa. minimum number of taxa per anchor reference
range. Ranges with fewer taxa will not be included
in the output node list.
- minTaxaPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
minimum number of taxa per anchor reference range.
Ranges with fewer taxa will not be included in the
output node list.
- minTaxaPerRange(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Min Taxa. minimum number of taxa per anchor reference
range. Ranges with fewer taxa will not be included
in the output node list.
- minTaxaPerRange() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
minimum number of taxa per anchor reference range. Ranges with fewer taxa will not be included in the output node list.
- minTaxaPerRange(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Min Taxa. minimum number of taxa per anchor reference range. Ranges with fewer taxa will not be included in the output node list.
- minTransitionProb() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
minimum probability of a transition between nodes at
adjacent reference ranges.
- minTransitionProb(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Min Transition Prob. minimum probability of a transition
between nodes at adjacent reference ranges.
- minTransitionProb() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
minimum probability of a transition between nodes at adjacent reference ranges.
- minTransitionProb(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Min Transition Prob. minimum probability of a transition between nodes at adjacent reference ranges.
- minTransitionProbability(minprob) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- minTransitionProbability() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
The minimum transition probability between a pair of
nodes in adjacent reference ranges.
- minTransitionProbability(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Min Transition Probability. The minimum transition
probability between a pair of nodes in adjacent reference
ranges.
- missing - Static variable in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- MostLikelyParents - Class in net.maizegenetics.pangenome.hapCalling
-
Given a set of read mappings, finds the most likely parents in a stepwise fashion. The parent with the most reads
is selected as a likely parent. Then the the subset of reads not mapping to that parent is created.
The parent with the most reads from that subset is then added to the list of likely parents.
The process is repeated until the number of likely parents = maxParents, coverage is equal to or greater than minCoverage,
or until all parents have been added to the list, whichever occurs first. Coverage is calculated as the number
of reads mapping to any of the likely parents divided by the total number of reads.
- MostLikelyParents(hapGraph) - Constructor for class net.maizegenetics.pangenome.hapCalling.MostLikelyParents
-
- MostLikelyParents(parentList, parentHapidMap) - Constructor for class net.maizegenetics.pangenome.hapCalling.MostLikelyParents
-
A constructor that takes a list of parents and for each
class ReferenceRange, a map of parent name to its hapid.
This constructor is intended mainly for unit testing.
- multinomialProbability(counts, probabilities) - Static method in class net.maizegenetics.pangenome.hapCalling.FindBestDiploidPathKt
-
- MultisampleBAMToMappingPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Plugin to load in multisample BAM based readMappings into the DB. This is effectively the same result as FastqToMappingPlugin or SAMToMappingPlugin.
- MultisampleBAMToMappingPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Plugin to load in multisample BAM based readMappings into the DB. This is effectively the same result as FastqToMappingPlugin or SAMToMappingPlugin.
- MultisampleBAMToMappingPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Plugin to load in multisample BAM based readMappings into the DB. This is effectively the same result as FastqToMappingPlugin or SAMToMappingPlugin.
- MultisampleBAMToMappingPlugin.ReadMappingResult - Class in net.maizegenetics.pangenome.hapCalling
-
- MultisampleBAMToMappingPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- Mummer4DoonerBZStats - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This method takes a coords file, the genome fastas, ranges to be covered Prints out tab-delimited file of metrics related to the region. THe output is tab-delimited, rows are anchors. columns are anchor-coordinates, covered coordinates (list, semicolon separated) percent covered.
- Mummer4DoonerBZStats() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- Mummer4DoonerBZStats(parentFrame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- Mummer4DoonerBZStats(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- mummer4Path() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Path where mummer4 executables live: nucmer, delta-filter,
show-snps, show-coords
- mummer4Path(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Set Mummer4 Executables Path. Path where mummer4 executables
live: nucmer, delta-filter, show-snps, show-coords
- mummer4Path() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Path to mummer4 binaries
- mummer4Path(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Set Mummer4 binary path
- MummerAnalysisMetricsPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
Deprecated.
- MummerAnalysisMetricsPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- MummerAnalysisMetricsPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- MummerAnalysisMetricsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- mummerParams() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Mummer parameters used
- mummerParams(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Set Mummer Parameters. Mummer parameters used
- mummerParams() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Parameters used when running mummer
- mummerParams(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Set Mummer Parameters. Value of parameters used when running mummer
- MummerScriptProcessing - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This class contains methods that run mummer4 scripts, e.g. nucmer, delta-filter, show-coords and show-snps. In addition, there are methods that process the output from these scripts. NOTE: processing here is relative to the needs of AssemblyHaplotypesPlugin.
- MutableKmerCounter - Class in net.maizegenetics.pangenome.hapCalling
-
Mutable version with ability to add individual kmers or whole sets of others KmerCounters
- MutableKmerCounter(sequence, kmerSize, stepSize, kmerPrefix) - Constructor for class net.maizegenetics.pangenome.hapCalling.MutableKmerCounter
-
Mutable version with ability to add individual kmers or whole sets of others KmerCounters
- MutableKmerToIdMap - Class in net.maizegenetics.pangenome.hapCalling
-
Mutable version of the KmerMap which allows for unique kmer->id mappings.
If a kmer is seen in multiple ids( or in the same id), its id in the map is set to -1
This datastructure can then be used to further purge out repetative kmers
- MutableKmerToIdMap(kmerSize, kmerPrefix) - Constructor for class net.maizegenetics.pangenome.hapCalling.MutableKmerToIdMap
-
Mutable version of the KmerMap which allows for unique kmer->id mappings.
If a kmer is seen in multiple ids( or in the same id), its id in the map is set to -1
This datastructure can then be used to further purge out repetative kmers
- mxDiv() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Maximum divergence.
- mxDiv(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Mx Div. Maximum divergence.
- myGVCFRangeToAlleleCallMap - Variable in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- myMissingAsRef - Variable in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- myPairedSimilarFragmentSort(pairedSimilarFragments, score, penalty, scoreThreshold) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.SyntenicAnchors
-
- myReferenceSequence - Variable in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
- old(args) - Static method in class net.maizegenetics.pangenome.GenerateHaplotypeCallerScripts
-
- otherData() - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- otherRegionsGroupName() - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
Name to give group of intervals not defined in the
user intervals file
- otherRegionsGroupName(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
Set Other Regions Group Name. Name to give group of
intervals not defined in the user intervals file
- outDir() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
Output directory path
- outDir() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
A directory to which output text files will be written.
This includes the summary statistics table as well as a file of minumum edit distances
for each sam/bam file processed.
- outDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
Set the output directory.
A directory to which output text files will be written.
This includes the summary statistics table as well as a file of minumum edit distances
for each sam/bam file processed.
- outExt() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
Type of file to output
- outFile() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
output metrics file. The tab-delimited file of summary statistcs calcualted from one or more gvcf files
Each file has a summary line in the table, as well as a line for each contig/chromosome
- outFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
Set output metrics file
output metrics file. The tab-delimited file of summary statistcs calcualted from one or more gvcf files
Each file has a summary line in the table, as well as a line for each contig/chromosome
- outFile() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Output file directory name, or new directory path; Directory will be created, if doesn't exist. Outfiles will be placed in the directory
- outFile(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Donor dir/file basename. Output file directory name, or new directory path; Directory will be created, if doesn't exist. Outfiles will be placed in the directory
- outPath() - Method in class net.maizegenetics.pangenome.api.WriteGraphAsGFAPlugin
-
Base file path for exported files. Enter a path without
file extensions. The plugin will append gfa and csv
to the output files.
- outPath(value) - Method in class net.maizegenetics.pangenome.api.WriteGraphAsGFAPlugin
-
Set Out Path. Base file path for exported files. Enter
a path without file extensions. The plugin will append
gfa and csv to the output files.
- output() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
File Name of the filtered read output
- output(value) - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
Set Output File. File Name of the filtered read output
- output() - Method in class net.maizegenetics.pangenome.hapcollapse.RankingFilePlugin
-
Output Ranking File.
- output(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RankingFilePlugin
-
Set Output. Output Ranking File.
- outputBAMDir() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Directory to point the script Template to for BAM writing.
If not specified, will be added to the
script and will need to be updated.
- outputBAMDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set Output BAM Directory. Directory to point the script
Template to for BAM writing. If not specified,
will be added to the script and will need to be updated.
- outputBamFile() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Name of the output filtered BAM/SAM file.
- outputBamFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Set Output Bam File. Name of the output filtered BAM/SAM
file.
- outputBase() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
base name for output files from this Plugin. Two files will be produced for each chromosome.
- outputBase(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Set Output file base. base name for output files from this Plugin. Two files will be produced for each chromosome.
- outputBedFile() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Output Bed file
- outputBedFile(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Output Bed File. Output Bed file
- outputDebugDir() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Directory to write out the read mapping files. This
is optional for debug purposes.
- outputDebugDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Debug Directory to write out read Mapping files..
Directory to write out the read mapping files. This
is optional for debug purposes.
- outputDebugDir() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Directory to write out the read mapping files. This
is optional for debug purposes.
- outputDebugDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Debug Directory to write out read Mapping files..
Directory to write out the read mapping files. This
is optional for debug purposes.
- outputDebugDir() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Directory to write out the read mapping files. This
is optional for debug purposes.
- outputDebugDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set Debug Directory to write out read Mapping files..
Directory to write out the read mapping files. This
is optional for debug purposes.
- outputDir() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
Directory where output files will be written
- outputDir(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
Set Output Directory. Directory where output files will be written
- outputDir() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Directory to write liquibase changeLogSync output
- outputDir(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Set Output Directory. Directory to write liquibase
changeLogSync output
- outputDir() - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
Path to write the split files
- outputDir(value) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
Set Output Directory. Path to write the split files
- outputDir() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
Directory to hold the output files.
- outputDir(value) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
Set Output Dir. Directory to hold the output files.
- outputDir() - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
Path to output directory where files will be written
- outputDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
Set Output Directory . Path to output directory where
files will be written
- outputDir() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Output Directory
- outputDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Set Output Dir. Output Directory
- outputDir() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
-
Deprecated.
Directory where you want to store the output VCFs
- outputDir(value) - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
-
Deprecated.
Set Output Dir. Directory where you want to store the output VCFs
- outputDir() - Method in class net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin
-
Directory path to output file indicating whether to
run liquibase.
- outputDir(value) - Method in class net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin
-
Set Output Directory. Directory path to output file
indicating whether to run liquibase.
- outputDir() - Method in class net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin
-
Directory path to write any liquibase output files.
- outputDir(value) - Method in class net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin
-
Set Output Directory. Directory path to write any liquibase
output files.
- outputDir() - Method in class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPlugin
-
Directory to which liquibase output and error files
will be written.
- outputDir(value) - Method in class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPlugin
-
Set Output Dir. Directory to which liquibase output
and error files will be written.
- outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
Full Path to which updated files will be written
- outputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
Set Output Directory. Full Path to which updated files
will be written
- outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Output directory including trailing / for writing files
- outputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
Set Output Directory. Output directory including trailing
/ for writing files
- outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Output directory including trailing / for writing files
- outputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Set Output Directory. Output directory including trailing / for writing files
- outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Output directory for writing files
- outputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Set Output Directory. Output directory for writing
files
- outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
Output fastq file to use as input for BWA-MEM
- outputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
Set Output File. Output fastq file to use as input for BWA-MEM
- outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Output directory including trailing / for writing files
- outputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Set Output Directory. Output directory including trailing / for writing files
- outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Output directory including trailing / for writing files
- outputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Set Output Directory. Output directory including trailing / for writing files
- outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
Output Directory
- outputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
Set Output Directory. Output Directory
- outputDir() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPlugin
-
Directory to output the processed PAF files
- outputDir(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPlugin
-
Set Output Directory. Directory to output the processed
PAF files
- outputDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- outputDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- outputFile() - Method in class net.maizegenetics.pangenome.api.ReferenceRangeSummaryPlugin
-
Output summary filename
- outputFile(value) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeSummaryPlugin
-
Set Output File. Output summary filename
- outputFile() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
-
Output filename
- outputFile(value) - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
-
Set Output File. Output filename
- outputFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
Name of output file to be written
- outputFile(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
Set Output File. Name of file to be written
- outputFile() - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
File for writing matrix of gene coverage
- outputFile(value) - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
Set Output File. File for writing matrix of gene coverage
- outputFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
Output GVCF File Path and Name.
- outputFile(value) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
Set Output G V C F File. Output GVCF File Path and Name.
- outputFile() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
FUll path to output file created by this plugin .
- outputFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
Set Output File. FUll path to output file created by this plugin .
- outputFile() - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
The file to which the output will be written. If the
file exists, an error will be thrown.
- outputFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
Set Out File. The file to which the output will be
written. If the file exists, an error will be thrown.
- outputFile() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
Output file name
- outputFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
Set Output VCF File Name. Output file name
- outputFile() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Output file name
- outputFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Set Output VCF File Name. Output file name
- outputFile() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
The name and path of the output file which will be
written by this plugin.
- outputFile(value) - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
Set Outfile. The name and path of the output file which
will be written by this plugin.
- outputFile() - Method in class net.maizegenetics.pangenome.io.PathsToFastaPlugin
-
Output base file name
- outputFile(value) - Method in class net.maizegenetics.pangenome.io.PathsToFastaPlugin
-
Set Output Base VCF File Name. Output base file name
- outputFile() - Method in class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
Output filename
- outputFile(value) - Method in class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
Set Output File. Output filename
- outputFile() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
File where metrics will be written.
- outputFile(value) - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
Set Directory to write out statistics files.. File
where metrics will be written.
- outputFile() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
Output File
- outputFile(value) - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
Set Output File. Output File
- outputFile() - Method in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
-
FUll path to output file created by this plugin .
- outputFile(value) - Method in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
-
Set Output File. FUll path to output file created by this plugin .
- outputFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
File for writing matrix of gene coverage
- outputFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
Set Output File. File for writing matrix of gene coverage
- outputFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
File for writing matrix of gene coverage
- outputFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
Set Output File. File for writing matrix of gene coverage
- outputFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
File where metrics will be written.
- outputFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
Set Output File. File where metrics will be written.
- outputFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
Path and name of file where tab-delimited output will
be written
- outputFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
Set Output File. Path and name of file where tab-delimited
output will be written
- outputFileDirectory() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
Output file directory
- outputFileDirectory(value) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
Set Output File Directory. Output file directory
- outputFileName() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
Name of output file
- outputFileName(value) - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
Set Output File. Name of output file
- outputFiltered() - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
If set to true, output the filtered name expected by
the snakemake script.
- outputFiltered(value) - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
Set Output Filtered File Name. If set to true, output
the filtered name expected by the snakemake script.
- outputGroupingFile() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
File to write out the groupings.
- outputGroupingFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set File To output the groupings which have been merged..
File to write out the groupings.
- outputIndexFile() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Index File Output.
- outputIndexFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Set Index File Output. Index File Output.
- outputJustGT() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Output just the GT flag. If set to false(default)
will output DP, AD and PL fields
- outputJustGT(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Set Output Just G T. Output just the GT flag. If set
to false(default) will output DP, AD and PL fields
- outputKeyFile() - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
Name of the output file to process.
- outputKeyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
Set Output KeyFile. Name of the output file to process.
- outputKeyFiles(keyFileName, keyFileLines, flowcellCol, phg, taxonCol, methodName, keyFileColumnNameMap) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to output mapping id and path key files to be used by the path finding.
- outputMapFile() - Method in class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
Output File Name. JSON file will be written
- outputMapFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
Set Output File Name. Output File Name. JSON file
will be written
- outputMergedFastqDir() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Directory to write out the fastq files.
- outputMergedFastqDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set Directory to write out merged fastq files.. Directory
to write out the fastq files.
- outputPathFindingKeyFile() - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Output Key File that can be used in path finding. This
is optional. If no file path is supplied, no file
will be written.
- outputPathFindingKeyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Set Output Key File. Output Key File that can be used
in path finding. This is optional. If no file path
is supplied, no file will be written.
- outputPathKeyFile() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Output Key File that can be used in path finding. This
is optional and will only be written if read mappings
are written to the database. If no file path is supplied
or mappings are written to file, no keyfile will be
written.
- outputPathKeyFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Set Output Key File. Output Key File that can be used
in path finding. This is optional and will only be
written if read mappings are written to the database.
If no file path is supplied or mappings are written
to file, no keyfile will be written.
- outputSamFiles() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Output SAM files instead of BAM files
- outputSamFiles(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set Output SAM Files. Output SAM files instead of BAM
files
- outputSecondaryMappingStats() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Ouptput Secondary Mapping Statistics such as total
AS for each haplotype ID
- outputSecondaryMappingStats(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Output secondary mapping statistics.. Ouptput Secondary
Mapping Statistics such as total AS for each haplotype
ID
- outputSecondaryMappingStats() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Ouptput Secondary Mapping Statistics such as total
AS for each haplotype ID
- outputSecondaryMappingStats(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Output secondary mapping statistics.. Ouptput Secondary
Mapping Statistics such as total AS for each haplotype
ID
- outputSecondaryMappingStats() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Ouptput Secondary Mapping Statistics such as total
AS for each haplotype ID
- outputSecondaryMappingStats(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set Output secondary mapping statistics.. Ouptput Secondary
Mapping Statistics such as total AS for each haplotype
ID
- outputSLURMScript() - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
Name of the Output SLURM Script
- outputSLURMScript(value) - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
Set Output SLURM Script. Name of the Output SLURM Script
- outputSplitFile() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
File to output the split contig file
- outputSplitFile(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
Set Output file. File to output the split contig file
- outputStatsFile() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Name of the output stats file of RefRange to total
counts.
- outputStatsFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Set Output Stats File. Name of the output stats file
of RefRange to total counts.
- outputTargetNameFile() - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
Name of the Output Target Name File
- outputTargetNameFile(value) - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
Set Output Target Name File. Name of the Output Target
Name File
- outputTaxaNames() - Method in class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
Output the Hapid -> TaxaName list Map.
- outputTaxaNames(value) - Method in class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
Set Output Taxa Names. Output the Hapid -> TaxaName
list Map.
- outputType() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Output GVCF typed files. If set to gvcf(default) it
will send all REFBlocks, SNPs and Indels. If set to
vcf, it will only output SNPs, Indels and missing values(if
fillGaps = true)
- outputType(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Set Output Type. Output GVCF typed files. If set to
gvcf(default) it will send all REFBlocks, SNPs and
Indels. If set to vcf, it will only output SNPs, Indels
and missing values(if fillGaps = true)
- outputVCFDir() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
Output VCF file directory.
- outputVCFDir(value) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
Set Output VCF Directory. Output VCF file directory.
- outVcfFile() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
The name of the file to be output by the PathsToVCFPlugin.
- outVcfFile(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Out Vcf File. The name of the file to be output
by the PathsToVCFPlugin.
- overwrite() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Overwrite
- overwrite(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Overwrite. Overwrite
- overwriteOutput() - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
If this is set to true and the output file exists,
it will be overwritten without warning.
- overwriteOutput(value) - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
Set Overwrite. If this is set to true and the output
file exists, it will be overwritten without warning.
- pairedEnd() - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
Should paired end reads be generated?
- pairedEnd(value) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
Set Paired End. Should paired end reads be generated?
- pairedMode() - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Run in paired mode. This will remove any haplotype
counts if they are not agreed by the pair.
- pairedMode(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
Set Paired. Run in paired mode. This will remove any
haplotype counts if they are not agreed by the pair.
- pairedMode() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
Run in paired mode. This will remove any haplotype
counts if they are not agreed by the pair.
- pairedMode(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
Set Paired. Run in paired mode. This will remove any
haplotype counts if they are not agreed by the pair.
- PairedSimilarFragment - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
Class that holds reference and assembly alignment data to be sorted and filtered in a longest path algorithm.
- PairedSimilarFragment(refStartPos, refEndPos, asmStartPos, asmEndPos, score, strand) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- pairFromIndex(index) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbabilityWithInbreeding
-
- pangenomeDir() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
The directory of the pangenome file and index.
- pangenomeDir(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Pangenome Dir. The directory of the pangenome file
and index.
- pangenomeDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- pangenomeDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- pangenomeHaplotypeMethod() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
The haplotype method used to create the pangenome.fa
and pangenome.mmi.
- pangenomeHaplotypeMethod(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Pangenome Haplotype Method. The haplotype method
used to create the pangenome.fa and pangenome.mmi.
- pangenomeIndexName() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
WARNING: By default the plugin will construct pangenome
file and index names from the pangenomeHaplotypeMethod.
Only use this parameter to over-ride that name with
a different one. Be sure the pangenomeHaplotypeMethod
matches the index.
- pangenomeIndexName(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Pangenome Index Name. WARNING: By default the plugin
will construct pangenome file and index names from
the pangenomeHaplotypeMethod. Only use this parameter
to over-ride that name with a different one. Be sure
the pangenomeHaplotypeMethod matches the index.
- pangenomePath - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- pangenomePathDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- parseBauerFlint(chromString) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- parseChangesetVersion(changeset) - Static method in class net.maizegenetics.pangenome.pipeline.PipelineUtilsKt
-
This function finds the PHG version from a changeset ID string.
The version should be the last value following the last underscore.
If there are no underscores, look up the change set in the map.
- parseChromAsRomanNumerals(chromString) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- parseChromFirstTab(chromString) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- parseChromosome(chromString) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- parseCoordinateRegions(coordFile, chromosome) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Method to parse out the reference coordinates into a map which along with the SNP data can then be used to create Variants.
- parseGCA(chromString) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- parseGVCFData(gvcfIdToRemotePath, LocalGVCFFolder) - Static method in class net.maizegenetics.pangenome.api.VariantUtils
-
This needs to return a Map of gvcfId to Tuple The remote path will be parsed later for downloading from servers.
- parseGVCFFileIntoRangeMap(gvcfFile) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Method to take the GVCF file and parse it into a RangeMap. Blocks of Reference sequence have a value of 'REFRANGE' which redirects to the Reference GenomeSequence Single SNPs are stored as single element ranges Indels are stored as well. Deletions generally take up multiple reference positions
- parseIndexLine(indexLine) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Simple function to parse the index lines quickly by using indexOf instead of String.split()
When I profiled this, split was taking a large amount of time. So to limit it, this was coded up.
Unsure of overall efficiency however and could likely be reverted to indexLine.split()
- parseKeyFile(keyfile) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
- parseKmerLine(currentString) - Static method in class net.maizegenetics.pangenome.hapCalling.KmerUtils
-
Function to parse the Kmer line. This just splits the currentLine and then will convert the characters to integers and then add them to an array
- parseMethodJsonParamsToString(methodDescription) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
Takes a passed method description string from a PHG dd methods table entry, and formats the JSON key/value pairs into a Map for the user. If the string does not parse to JSON, a single map entry of "notes":methodDescription will be created and returned.
- parseMummerSNPFile(fileName, chromosome) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Method to parse the Mummer SNP file into a rangemap The first String in the tuple is for the reference call The second String is for the assembly call
- parseVariantContextsIntoRangeMap(variantContexts, taxonName) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFGenotypeSequence
-
Method to parse the variantContexts into a RangeMap correctly for the genotype case
- parseVariantContextsIntoRangeMap(variantContexts, taxonName) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Method to parse the variantContexts into rangeMap for a single taxon. This will simply call parseVariantContextsIntoRangeMap but with a gameteIndex of 0
- parseVariantContextsIntoRangeMap(variantContexts, taxonName, gameteIndex) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Method to parse the List of variantContexts into the rangemap required by this class. Allows you to build the GVCFSequence from memory.
- parseVariantInfosIntoRangeMap(variantInfos) - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Method to parse the List of variantContexts into the rangemap required by this class. Allows you to build the GVCFSequence from memory.
- password() - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
Password for database
- password(value) - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
Set Password. Password for database
- password() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
Password for database
- password(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
Set Password. Password for database
- path(paths) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
-
Returns sorted set of haplotype ids from the given paths.
- path(taxon, nodes) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns most probable
class HaplotypePath for each
Chromosome given the specified taxon and list of known
class HaplotypeNodes. List of nodes can have at most one node per
class ReferenceRange. Nodes constructed with specified taxon will always be used in resulting paths. Specified nodes must either have been constructed with specified taxon or reside in a reference range that has no node constructed with specified taxon.
- path(taxon, nodes) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns most probable
class HaplotypePath for each
Chromosome given the specified
Taxon and list of known
class HaplotypeNodes. List of nodes can have at most one node per
class ReferenceRange. Nodes constructed with specified taxon will always be used in resulting paths. Specified nodes must either have been constructed with specified taxon or reside in a reference range that has no node constructed with specified taxon.
- path(nodes) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
- path(taxon) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns most probable
class HaplotypePath for each
Chromosome given the specified taxon. Nodes constructed with specified taxon will always be used in resulting paths.
- path(taxon) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns most probable
class HaplotypePath for each
Chromosome given the specified
Taxon. Nodes constructed with specified taxon will always be used in resulting paths.
- path() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
- pathFile() - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
File Holding the path
- pathFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
Set Path File. File Holding the path
- PathFinderForSingleTaxonNodes - Class in net.maizegenetics.pangenome.hapCalling
-
- PathFinderForSingleTaxonNodes(inputGraph, readMap, probCorrect, sameGameteProbability, minReadsPerRange, maxReadsPerKB, removeEqual, inbreedCoef, parentList, useLikelyParents, parentFinder, maxParents, minCoverage) - Constructor for class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes
-
- PathFinderForSingleTaxonNodesFactory - Class in net.maizegenetics.pangenome.hapCalling
-
- PathFinderForSingleTaxonNodesFactory(graph, sameGameteProbability, requiredTaxaList, probCorrect, minTaxaPerRange, minReadsPerRange, maxReadsPerKB, removeEqual, inbreedCoef, maxParents, minCoverage) - Constructor for class net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory
-
- PathFindingInput(keyFileEntry, readMappingCounts) - Constructor for class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingInput
-
- PathFindingInput(keyFileEntry, readMappingCounts) - Constructor for class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingInput
-
- PathFindingResult(keyFileEntry, path, likelyParents, totalReads) - Constructor for class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- PathFindingResult(keyFileEntry, path, likelyParents, totalReads) - Constructor for class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- pathHapids(configFile, pathFileNames) - Static method in class net.maizegenetics.pangenome.api.RMethods
-
- pathHaplotypeMethod() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
The haplotype method used to impute a path. The same
method will be used to create the PHG used for read
mapping.
- pathHaplotypeMethod(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Path Haplotype Method. The haplotype method used
to impute a path. The same method will be used to create
the PHG used for read mapping.
- pathInfoFilename() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
The name of the file to which detailed path diagnostic information will be written. If the name is not supplied the diagnotic information will not be reported. The target taxon name must be supplied as well.
- pathInfoFilename(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Path Info File. The name of the file to which detailed path diagnostic information will be written. If the name is not supplied the diagnotic information will not be reported. The target taxon name must be supplied as well.
- pathMethod() - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
Gametes from this path method will be added to the
HaplotypeGraph.
- pathMethod(value) - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
Set Path Method. Gametes from this path method will
be added to the HaplotypeGraph.
- pathMethod() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
Gametes from this path method will be added to the
HaplotypeGraph.
- pathMethod(value) - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
Set Path Method. Gametes from this path method will
be added to the HaplotypeGraph.
- pathMethod() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
Name of method used to create paths, as it should appear in the paths table
- pathMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
Set Path Method. Name of method used to create paths, as it should appear in the paths table
- pathMethod() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Name of method to be used to create paths through the graph.
- pathMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Set P Method. Name of method to be used to create paths through the graph.
- pathMethodDescription() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
An additional description that will be stored with
the path method name, if desired.
- pathMethodDescription(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Path Method Description. An additional description
that will be stored with the path method name, if desired.
- pathMethodDescription() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
An additional description that will be stored with
the path method name, if desired.
- pathMethodDescription(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Path Method Description. An additional description
that will be stored with the path method name, if desired.
- pathMethodDetails() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
Description of method used to create paths - optional
- pathMethodDetails(value) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
Set Path Method Details. Description of method used to create paths - optional
- pathMethodName() - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
-
Path Method Name Stored in the DB
- pathMethodName(value) - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
-
Set Path Method Name. Path Method Name Stored in the DB
- pathMethodName() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
The name of the path method used to write the results
to the PHG DB
- pathMethodName(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Path Method. The name of the path method used to
write the results to the PHG DB
- pathMethodName() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
The name of the path method used to write the results
to the PHG DB
- pathMethodName(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Path Method. The name of the path method used to
write the results to the PHG DB
- pathMethodName() - Method in class net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin
-
Path Method Name Stored in the DB
- pathMethodName(value) - Method in class net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin
-
Set Path Method Name. Path Method Name Stored in the
DB
- pathMethodName() - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
-
Deprecated.
Path Method Name Stored in the DB
- pathMethodName(value) - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
-
Deprecated.
Set Path Method Name. Path Method Name Stored in the DB
- pathName() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
Name of method used for create PHG Path. Should match the assembly path method - that default is mummer4_PATH
- pathName(value) - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
Set Path Method Name. Name of method used for create PHG Path. Should match the assembly path method - that default is mummer4_PATH
- pathName() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
The path method name assigned when the path was created and stored in the DB. Not required if a path file name is supplied.
- pathName(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Set Path method name. The path method name assigned when the path was created and stored in the DB. Not required if a path file name is supplied.
- pathName() - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
The name to give this path in the database
- pathName(value) - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
Set Path Name. The name to give this path in the database
- pathOutDirectory() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Directory to which path files will be written.
- pathOutDirectory(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Read Map Directory. Directory to which path files
will be written.
- pathsDir() - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
-
Paths directory
- pathsDir(value) - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
-
Set Paths Directory.
- pathsForMethod(configFile, pathMethod) - Static method in class net.maizegenetics.pangenome.api.RMethods
-
- PathsToFastaPlugin - Class in net.maizegenetics.pangenome.io
-
This exports paths to a Fasta file(s).
- PathsToFastaPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.io.PathsToFastaPlugin
-
This exports paths to a Fasta file(s).
- PathsToFastaPlugin() - Constructor for class net.maizegenetics.pangenome.io.PathsToFastaPlugin
-
This exports paths to a Fasta file(s).
- pathsToNodes(paths) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
-
- PathsToVCFHaplotypesPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
This exports diploid or haploid paths to a VCF file with haplotype allele values (Not SNPs).
- PathsToVCFHaplotypesPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
This exports diploid or haploid paths to a VCF file with haplotype allele values (Not SNPs).
- PathsToVCFHaplotypesPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
This exports diploid or haploid paths to a VCF file with haplotype allele values (Not SNPs).
- PathsToVCFPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
This exports diploid or haploid paths to a VCF file.
- PathsToVCFPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
This exports diploid or haploid paths to a VCF file.
- PathsToVCFPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
This exports diploid or haploid paths to a VCF file.
- pathTaxaList() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
Only gametes from these taxa will be added to the graph.
If null, then all gametes will be added for the path
method.
- pathTaxaList(value) - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
Set Path Taxa List. Only gametes from these taxa will
be added to the graph. If null, then all gametes will
be added for the path method.
- PathToGFFPlugin - Class in net.maizegenetics.pangenome.annotations
-
THis class takes a keyfile with taxon to gff-path mapping, a taxon name and a method.
It creates a haplotype graph from the path obtained
- PathToGFFPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
THis class takes a keyfile with taxon to gff-path mapping, a taxon name and a method.
It creates a haplotype graph from the path obtained
- PathToGFFPluginKt - Class in net.maizegenetics.pangenome.annotations
-
- PathToIgraphPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Deprecated.
- PathToIgraphPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
- percentPerChromGFFBasePairs(gffSet) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
- percentPerChromNonGFFBasePairs(gffSet) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
- phasingConfidence() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
-
- PHGData - Interface in net.maizegenetics.pangenome.db_loading
-
- PHGDataWriter - Interface in net.maizegenetics.pangenome.db_loading
-
- PHGdbAccess - Class in net.maizegenetics.pangenome.db_loading
-
Access methods for postgres or SQL PHG dbs. WHen making changes, or adding new methods, test the SQL statements in both PostgreSQL and SQL to ensure compatibility.
- PHGdbAccess(dbConnection) - Constructor for class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- phgDBName - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- phgDBNameDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- phgDBNamePostgres - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- PHGtoGFAv1Plugin - Class in net.maizegenetics.pangenome.io
-
This plugin exports a PHG Graph to GFAv1 format.
PHG Paths can also be included if "Walk Lines" are wanted in the file.
http://gfa-spec.github.io/GFA-spec/GFA1.html
- PHGtoGFAv1Plugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
This plugin exports a PHG Graph to GFAv1 format.
PHG Paths can also be included if "Walk Lines" are wanted in the file.
http://gfa-spec.github.io/GFA-spec/GFA1.html
- PHGtoGFAv1Plugin() - Constructor for class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
This plugin exports a PHG Graph to GFAv1 format.
PHG Paths can also be included if "Walk Lines" are wanted in the file.
http://gfa-spec.github.io/GFA-spec/GFA1.html
- PipelineUtilsKt - Class in net.maizegenetics.pangenome.pipeline
-
- ploidy() - Method in class net.maizegenetics.pangenome.db_loading.GenoHaploData
-
- pluginDescription() - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
-
- pluginDescription() - Method in class net.maizegenetics.pangenome.api.WriteGraphAsGFAPlugin
-
- pluginDescription() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
-
- pluginDescription() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
- pluginDescription() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
- pluginDescription() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
- pluginDescription() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
- pluginDescription() - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
- pluginDescription() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
- pluginDescription() - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
- pluginDescription() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
- pluginDescription() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
- pluginDescription() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
- pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
-
Deprecated.
- pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
- pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
- pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
- pluginUserManualURL() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
- plusAssign(newKmerCounts) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerCounter
-
- PopulatePHGDBPipelinePlugin - Class in net.maizegenetics.pangenome.pipeline
-
This class creates a pipeline that will load an existing PHG database with assembly and/or WGS haplotypes.
It is not recommended for use when anchorwave is the assembly alignment method. Anchorwave uses both
alot of memory and alot of computing power. We recommend users align with anchorwave on high performance/
high memory machines. THe generated MAF files can then be run through MAFToGVCFPlugin, followed by
LoadHapltoypesFromGVCFPlugin.
- PopulatePHGDBPipelinePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
This class creates a pipeline that will load an existing PHG database with assembly and/or WGS haplotypes.
It is not recommended for use when anchorwave is the assembly alignment method. Anchorwave uses both
alot of memory and alot of computing power. We recommend users align with anchorwave on high performance/
high memory machines. THe generated MAF files can then be run through MAFToGVCFPlugin, followed by
LoadHapltoypesFromGVCFPlugin.
- PopulatePHGDBPipelinePlugin() - Constructor for class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
This class creates a pipeline that will load an existing PHG database with assembly and/or WGS haplotypes.
It is not recommended for use when anchorwave is the assembly alignment method. Anchorwave uses both
alot of memory and alot of computing power. We recommend users align with anchorwave on high performance/
high memory machines. THe generated MAF files can then be run through MAFToGVCFPlugin, followed by
LoadHapltoypesFromGVCFPlugin.
- PopulatePHGDBPipelinePlugin.ASSEMBLY_ALIGNER - Enum in net.maizegenetics.pangenome.pipeline
-
- PopulatePHGDBPipelinePluginKt - Class in net.maizegenetics.pangenome.pipeline
-
- position() - Method in class net.maizegenetics.pangenome.api.Variant
-
- position() - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- positions() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
Positions to include in VCF. Can be specified by Genotype
file (i.e. VCF, Hapmap, etc.), bed file, or json file
containing the requested positions.
- positions(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
Set Position List. Positions to include in VCF. Can
be specified by Genotype file (i.e. VCF, Hapmap, etc.),
bed file, or json file containing the requested positions.
- positions() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Positions to include in VCF. Can be specified by Genotype
file (i.e. VCF, Hapmap, etc.), bed file, or json file
containing the requested positions.
- positions(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Set Position List. Positions to include in VCF. Can
be specified by Genotype file (i.e. VCF, Hapmap, etc.),
bed file, or json file containing the requested positions.
- PositionToRefAndAltHaplotypes - Class in net.maizegenetics.pangenome.hapCalling
-
- PositionToRefAndAltHaplotypes() - Constructor for class net.maizegenetics.pangenome.hapCalling.PositionToRefAndAltHaplotypes
-
- postgresContainer - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- postgresDataDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- postgresDockerDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- postgresDockerfile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- postgresHost - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- postgresImageName - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- postgresPort - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- postgresUser - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- postgresUserPwd - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- postProcessParameters() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
- postProcessParameters() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
- postProcessParameters() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
- prefix() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Name to prefix to output results file
- prefix(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Set Output File refix. Name to prefix to output results file
- prefix() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Name to prefix to output results file
- prefix(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Set Output File refix. Name to prefix to output results file
- preProcessParameters(input) - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
- preProcessParameters(input) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
- preProcessParameters(input) - Method in class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
- presenceAbsenceTaxonByNode(graph, filename) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
-
- previousRange(range) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
- printTrimTables(origData, trimData, outputFile) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- probabilityCorrect(pcorrect) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability.Builder
-
- probabilityCorrect() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
The probability that a read mapped to the correct haplotypes
- probabilityCorrect(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Probability Correct. The probability that a read
mapped to the correct haplotypes
- probabilityOfBeingCorrect(hapGraph, hapidCounts) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- probabilityOfBeingCorrect(hapidCounts, rangeToNodesMap) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- probabilityOfBeingCorrect(hapidCountMap, rangeToNodesMap) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- probabilityReadMappingCorrect(probCorrect) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- probReadMappedCorrectly() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
minimum number of reads per anchor reference range.
Ranges with fewer reads will not be included in the
output node list.
- probReadMappedCorrectly(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Prob Correct. minimum number of reads per anchor
reference range. Ranges with fewer reads will not be
included in the output node list.
- probReadMappedCorrectly() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
- probReadMappedCorrectly(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Prob Correct. minimum number of reads per anchor reference range. Ranges with fewer reads will not be included in the output node list.
- processCreateHash(inputFile, digestType) - Static method in class net.maizegenetics.pangenome.Utils.CreateHashForFiles
-
- processData(input) - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphStreamBuilderPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.api.MethodTableReportPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.api.ReadMethodTablePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeSummaryPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.api.WriteFastaFromGraphPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.api.WriteGraphAsGFAPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.ChangeDBMethodTypePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.CloseDBConnectionPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.CreateGeneIntervalsFromConservedGFFPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.CreatePHGPostgresDockerPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.DatabaseSummaryPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.GetDBConnectionPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.db_updateDelete.DeleteReadMappingPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.gui.ViewGraphPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFSingleFilePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
Plugin method to process the data
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.CreateHapIdMapsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.FastqDirToMappingPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.ImportHaplotypePathFilePlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypeKmersPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.IndexHaplotypesBySNPPlugin
-
Method to index the PHG for each SNP specified in the vcfFile
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapcollapse.CentroidPathFromGraphPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Method to create a consensus haplotype GenotypeTable object Method will now just create and return the GenotypeTable instead of doing additional work to create the fasta sequence.
- processData(input) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapcollapse.RankingFilePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.io.PathsToFastaPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.pipeline.LiquibaseCommandPlugin
-
Function to run specified liquibase commands, return value
- processData(input) - Method in class net.maizegenetics.pangenome.pipeline.MakeDefaultDirectoryPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.pipeline.MakeInitialPHGDBPipelinePlugin
-
Function to run the steps previously done by LoadGenomeIntervals.sh
- processData(input) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.pipelineTests.CompareToKnownSNPPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.pipelineTests.CountNsInRawHapSequencesPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataMetricsPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHapMetricPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateContigFastaFromAssemblyGenomePlugin
-
- processData(shortSeqs, assemblyDir, outputDir) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPlugin
-
For each line in the PAF file, the aligned number of 'contig' coordinates is compared to the edit distance.
If NM/numSites < our current NMthreshold, that aligned region is loaded into a RangeSet.
The RangeSet will merge any overlapping regions.
Then once all the mappings have been processed, this walks through each contig and determines
how many of the bps of the full contig were mapped with a good enough NM. These values are output to a file created in outputDir.
- processData(input) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
Method to split up each contig into splitSize'd chunks. If contig.length < splitSize, the contig is not chunked.
- processData(input) - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
- processDecimal(decimal, lastNumber, lastDecimal) - Static method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- processHaplotypesData(gamete_grp_id, method, anchorSequences, chromosome, genomeFileId, gvcfFileId) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- processMain(regexDataFile, origRefAnchors, outputFile) - Static method in class net.maizegenetics.pangenome.db_loading.CreateCSV_TrimmedAnchorLoading
-
- processMain(db, refLine, outputFile) - Static method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFile
-
- processMain(refFasta, trimmedFastas, outputDir, lineName) - Static method in class net.maizegenetics.pangenome.db_loading.FindTrimmedAnchorCoordinates
-
- processMain(assemblyFasta, trimmedFastas, outputDir, lineName) - Static method in class net.maizegenetics.pangenome.db_loading.FindTrimmedAssemblyCoordinates
-
- processMain(assemblyNameFile, outputFile, gvcf, variants) - Static method in class net.maizegenetics.pangenome.db_loading.ShellScript_createLoadHaplotypes
-
- processReadDirectory(readDir, graph) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Method that gets a list of read mapping files from the read directory and calls processReadFile
for each of the files.
- processReadFile(readFileName, graph) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Method to process a single read file and write the resulting path to the output directory.
If overwrite = false, then the method will not overwrite an existing path file.
- processSAMRecords(samReader, pairedEnd, hapIdToRefRangeMap, maxRefRangeError, outputBamFile, outputStatsFile) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Function that processes the records within a SAM file similar to what is done in Minimap2Utils.
This will keep track of the alignment stats as it is going and will output the correct values.
- ProfileInput(refRange, nodeList) - Constructor for class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileInput
-
- ProfileMxdivPlugin - Class in net.maizegenetics.pangenome.hapcollapse
-
Using a HaplotypeGraph supplied as input, this plugin evaluates how many consensus haplotypes
would be created for each ReferenceRange at different values of mxDiv.
It works by walking the UPGMA tree and reporting, for each internal node, the number of branches that exist at that height.
The number of branches corresponds to the number of haplotype nodes. The plugin can use either SNP distance or
KMER distance to construct the trees. SNP requires that the graph includes variants. KMER requires that the graph
includes sequence.
- ProfileMxdivPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
Using a HaplotypeGraph supplied as input, this plugin evaluates how many consensus haplotypes
would be created for each ReferenceRange at different values of mxDiv.
It works by walking the UPGMA tree and reporting, for each internal node, the number of branches that exist at that height.
The number of branches corresponds to the number of haplotype nodes. The plugin can use either SNP distance or
KMER distance to construct the trees. SNP requires that the graph includes variants. KMER requires that the graph
includes sequence.
- ProfileMxdivPlugin() - Constructor for class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin
-
Using a HaplotypeGraph supplied as input, this plugin evaluates how many consensus haplotypes
would be created for each ReferenceRange at different values of mxDiv.
It works by walking the UPGMA tree and reporting, for each internal node, the number of branches that exist at that height.
The number of branches corresponds to the number of haplotype nodes. The plugin can use either SNP distance or
KMER distance to construct the trees. SNP requires that the graph includes variants. KMER requires that the graph
includes sequence.
- ProfileMxdivPlugin.DistanceType - Enum in net.maizegenetics.pangenome.hapcollapse
-
- ProfileMxdivPlugin.ProfileInput - Class in net.maizegenetics.pangenome.hapcollapse
-
- ProfileMxdivPlugin.ProfileResult - Class in net.maizegenetics.pangenome.hapcollapse
-
- ProfileMxdivPluginKt - Class in net.maizegenetics.pangenome.hapcollapse
-
- ProfileResult(refRange, pairList) - Constructor for class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileResult
-
- purgeOutputFile() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Purge Array export after marking file.
- purgeOutputFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Set Purge Array Export. Purge Array export after marking
file.
- PurgeSequencesFromAlignments - Class in net.maizegenetics.pangenome.hapcollapse
-
Created by edbuckler on 6/19/17.
- put(kmer, id) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerToIdMap
-
Basic put function for String kmer and its associated id
- put(kmerAsByte, id) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerToIdMap
-
Put function taking in a ByteArray representation of the kmer and its associated id
- put(kmer, id) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerToIdMap
-
Put function from a Long Representation of the kmer and its Id
We apply the lambda here which will set the id to -1 if we have already seen this Id
- putAll(newKmerMap) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerToIdMap
-
Loop through the KmerMap and put each key-value pair into the existing map.
- putAll(kmerSet, id) - Method in class net.maizegenetics.pangenome.hapCalling.MutableKmerToIdMap
-
Method to add in all the kmers stored in a primitive Long Set into the kmerToIdMap using the input id.
- putAllAnchors(anchorData, refGroupMethodID) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Stores chrom, start pos, end pos to referenece_ranges table isFocus identifies focus intervals from the user's bed file
- putAllAnchors(adata, refGroupMethodID) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putAssemblyInterAnchorSequences(line_name, hapNumber, method, anchorSequences) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Adds inter-anchor sequences for the specified assembly to the anchor_sequences and anchor_haplotypes table. This method takes a multi-map as assembly. Inter-anchors that do not map to a reference inter-anchor are all given the anchorid 0.
- putAssemblyInterAnchorSequences(line_name, hapNumber, method, anchorSequences) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putConsensusSequences(consensusMap, methodId) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
This method takes a map of consensus data, finds the anchorIds based on Position, finds the hapids of the taxa whose sequences at the specified anchorID map to the consensus. Adds the gamete_group and sequence data to the haplotpes table ; adds entries to gamete_groups and gamete_hapltoypes. *
- putConsensusSequences(consensusMap, method_id) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putGameteGroupAndHaplotypes(gametes) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Takes a list of gametes and stores to the gamete_groups and gamete_haplotypes table Skips if this grouping already exists
- putGameteGroupAndHaplotypes(gametes) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putGenoAndHaploTypeData(ghData) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Stores required data to the genotypes and haplotypes tables for each entry on the list.
- putGenoAndHaploTypeData(ghData) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putGenomeFileData(genome_path, genome_file, genoid, type) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Method takes information on a genome fasta file, stores to the PHG db, returns the genome_file_data entry id created for the table entry.
- putGenomeFileData(genome_server_path, genome_file, genoid, type) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putHalotypeListData(hapids) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
put data to the haplotype Lists table.
- putHalotypeListData(hapids) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putHaplotypeCountsData(method, methodDetails, taxonName, fastqFile, counts) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
This method adds data to the haplotype_counts table. The "data" is a Snappy compressed byte buffer of a 3xn array, found in parameter "counts" To see how this data is stored, examine DBLoadingUtils.encodeHapCountsArrayFromFile(), DBLoadingUtils.encodeHapCountsArrayFromMultiset() and DBLoadingUtils.decodeHapCountsArray()
- putHaplotypeCountsData(method, methodDetails, taxonName, fastqFile, counts) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putHaplotypesData(gamete_grp_id, method, anchorSequences, chromosome, genomeFileId, gvcfFileId) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome and a genomeFileId. Starts the process of storing table data for the haplotypes to the db. This will set maxEntries to 10000 and will call the putHaplotypesData version below putHaplotypesData(int gamete_grp_id, int method, Map anchorSequences, String chromosome, int genomeFileId, gvcfFIleId)
- putHaplotypesData(gamete_grp_id, method, anchorSequences, chromosome, genomeFileId, gvcfFileId, maxEntries) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Takes a gamete_grp_id, method_id, list of haplotype sequences, a chromosome, genomeFileId, and a number of MaxEntries. Starts the process of storing table data for the haplotypes to the db
- putHaplotypesData(gamete_grp_id, method, anchorSequences, chromosome, genomeFileId, gvcfFileId) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putHaplotypesData(gamete_grp_id, method, anchorSequences, chromosome, genomeFileId, gvcfFileId, maxEntries) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putHaplotypesForGamete(gamete_grp_id, method, anchorSequences, genomeFileId, gvcfFileId) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Stores gamete sequence data to the haplotypes table This method associates all entries with the single gamete_grp_id which is passed in. It is used when loading reference_ranges sequences or haplotype sequences for a single line. THe gidToVariantDataMap map is used to create the variant list blob for the db
- putHaplotypesForGamete(gamete_grp_id, method_id, anchorSequences, genomeFileId, gvcfFileId) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putHaplotypesForMultipleGroups(mapWithGroupHash, method_id) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Add data to the haplotypes table. Entries on the map are for different gamete groups. The key is a Position item identifying the genome_interval id The value is a Tuple consisting of (x) AnchorDataPHG object with sequence, gvcf, etc; and (y) a List of taxa represented by the ANchorDataPHG sequence
- putHaplotypesForMultipleGroups(mapWithGroupHash, method_id) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putMethod(name, type, description) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Adds a method, its type and its description to the anchor_methods table These are used to identify how sequences were created,how the were combined into consensus sequences, how haplotype counts were scores, how paths through the graph were create or how an edge was created. The "type" field identifies the table to which the method belongs.
- putMethod(name, type, descriptionMap) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putPathsData(method, methodDetails, taxon, readMappingIds, pathBytes, isTestMethod) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
This method stores paths data to the paths table.
- putPathsData(method, methodDetails, taxon, readMappingIds, pathBytes, isTestMethod) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putReadMappingData(method, methodDetails, taxon, file_group_name, mapping_data, isTestMethod, haplotypeListId) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Takes a method name, method details string, taxon name (should exist in the genotypes table), file_group_name, and a byte array of read mapping data. This is stored to the PHG read_mapping table
- putReadMappingData(method, methodDetails, taxon, file_group_name, mapping_data, isTestMethod, haplotypeListId) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putRefAnchorData(line_name, hapnumber, adata, hapMethod, refGroupMethod, gvcf, variant_list, genomeFileId, gvcfFileId) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Fills in the haplotypes table for the reference ranges.
- putRefAnchorData(line_name, hapnumber, anchorData, hapMethod, refGrpMethods, gvcf, variant_list, genomeFileId, gvcfFileId) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putRefRangeRefRangeMethod(group_method_id, refRangeList) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Takes a method id and a list of reference ranges. Populates the ref_range_ref_range_method table.
- putRefRangeRefRangeMethod(method_id, refRangeIDList) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putTaxaGroupName(group_name) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Creates an entry in the taxa_groups table. If one already exists with the specified name, the id for it is returned.
- putTaxaGroupName(group_name) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- putTaxaTaxaGroups(group_name, taxaList) - Method in interface net.maizegenetics.pangenome.db_loading.PHGDataWriter
-
Takes a taxa group name and a list of taxa. Populates the taxa_groups and taxa_groups_genoid tables.
- putTaxaTaxaGroups(group_name, taxaList) - Method in class net.maizegenetics.pangenome.db_loading.PHGdbAccess
-
- RampSeqContigToGenomeIntervalPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
Deprecated.
- RampSeqContigToGenomeIntervalPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
- RampSeqContigToGenomeIntervalPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
- RampSeqContigToGenomeIntervalPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.RampSeqContigToGenomeIntervalPlugin
-
Deprecated.
- ranges() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
Tab-delimited, BED Formatted file containing chrom, ref range start position, ref range end position. No header line.
- ranges(value) - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeGroupPlugin
-
Set Ranges File. Tab-delimited, BED Formatted file containing chrom, ref range start position, ref range end position. No header line.
- rangeSetFromHapidSet(hapids, hapidRangeMap) - Static method in class net.maizegenetics.pangenome.api.RMethods
-
- rangesFromPositions(positions) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MafUtils
-
- rankingFile() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
File The Ranking for the Taxon in the DB. This is used to break ties.
- rankingFile(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Ranking File. File The Ranking for the Taxon in the DB. This is used to break ties.
- rankingFile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- rankingFileDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- RankingFilePlugin - Class in net.maizegenetics.pangenome.hapcollapse
-
- RankingFilePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapcollapse.RankingFilePlugin
-
- RankingFilePlugin() - Constructor for class net.maizegenetics.pangenome.hapcollapse.RankingFilePlugin
-
- RankingFilePluginKt - Class in net.maizegenetics.pangenome.hapcollapse
-
- readAnchorIds() - Static method in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
-
Reads in list of anchor region numbers that are IBD
- readDir() - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
Name of the Fasta/Fastq dir to process.
- readDir(value) - Method in class net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin
-
Set Fasta or Fastq dir to process. Name of the Fasta/Fastq
dir to process.
- readFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
-
Deprecated.
Raw Read file aligned to the reference
- readFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToKmerCountPlugin
-
Deprecated.
Set Raw Read File. Raw Read file aligned to the reference
- readGFFtoGff3Feature(gffFile) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Function to use htsjdk to read gff into memory.
Returns a Set .
- readInKeyFile(fileName) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to read in the key file. The first of the pair is the column mapping and the second is a 2-d list.
- readInListOfMultimapHits(inputFiles, graph) - Static method in class net.maizegenetics.pangenome.hapCalling.ReadMappingUtils
-
Function to read in the multimap Hits from a file and store it in a list. The graph is needed to get a refRangeId to RefRange mapping
- readInListOfMultimapHits(inputFiles, rangeIdToRangeMap) - Static method in class net.maizegenetics.pangenome.hapCalling.ReadMappingUtils
-
Function to read in the Multimap
- readInMultimapHits(inputFileName, graph) - Static method in class net.maizegenetics.pangenome.hapCalling.ReadMappingUtils
-
Function to read in the multimap Hits from a file and store it in a Multimap. The graph is needed to get a refRangeId to RefRange mapping
- readInMultimapHits(inputFileName, rangeIdToRangeMap) - Static method in class net.maizegenetics.pangenome.hapCalling.ReadMappingUtils
-
Function to read in the multimap hits.
- readInMultimapHitsFromFile(inputFileName) - Static method in class net.maizegenetics.pangenome.hapCalling.ReadMappingUtils
-
Function to read in the multimapHits from a text file.
- readInReadMappings(inputFileName, graph) - Static method in class net.maizegenetics.pangenome.hapCalling.ReadMappingUtils
-
- readLength() - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
length of reads to be generated
- readLength(value) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
Set Read Length. length of reads to be generated
- readLength() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Desired length of reads for fastq files
- readLength(value) - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Set Length Of Reads. Desired length of reads for fastq files
- readMap(readMap) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- readMapDirectory() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Directory of read mapping files. If this is supplied,
do not also assign a read filename.
- readMapDirectory(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Read Map Directory. Directory of read mapping files.
If this is supplied, do not also assign a read filename.
- readMapFilename() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Filename of read mappings. Do not supply both a filename
and a directory.
- readMapFilename(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Read Map File. Filename of read mappings. Do not
supply both a filename and a directory.
- ReadMappingDBRecord - Class in net.maizegenetics.pangenome.db_loading
-
- ReadMappingDBRecord(methodName, methodDetails, readMappingId, readMappings, genoName, fileGroupName) - Constructor for class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- ReadMappingDecoder - Class in net.maizegenetics.pangenome.hapCalling
-
ReadMappingDecoder gets an encoded read mapping from a database based on a read mapping id and
decodes it to return counts of haplotype id sets as a map (Map>). It correctly decodes either BitSet
encoded haplotype set counts or the older format without BitSet encoding.
The class has two constructors.
One of them takes a PHGdbAccess object and the other takes no arguments and instantiates a PHGdbAccess object based
on connection parameters stored in the ParameterCache.
- ReadMappingDecoder(phgAccess) - Constructor for class net.maizegenetics.pangenome.hapCalling.ReadMappingDecoder
-
ReadMappingDecoder gets an encoded read mapping from a database based on a read mapping id and
decodes it to return counts of haplotype id sets as a map (Map>). It correctly decodes either BitSet
encoded haplotype set counts or the older format without BitSet encoding.
The class has two constructors.
One of them takes a PHGdbAccess object and the other takes no arguments and instantiates a PHGdbAccess object based
on connection parameters stored in the ParameterCache.
- ReadMappingDecoder() - Constructor for class net.maizegenetics.pangenome.hapCalling.ReadMappingDecoder
-
- ReadMappingInputFileFormat - Enum in net.maizegenetics.pangenome.hapCalling
-
- ReadMappingKeyFileParsed - Class in net.maizegenetics.pangenome.hapCalling
-
- ReadMappingKeyFileParsed(keyFileRecordsToFileMap, fileNameToPathMap, keyFileColumnNameMap, keyFileLines) - Constructor for class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- readMappingMethod() - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Read Mapping Method in the DB. Must be consistent
across all DBs/files
- readMappingMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.ImportReadMappingToDBPlugin
-
Set Read Mapping Method. Read Mapping Method in the
DB. Must be consistent across all DBs/files
- readMappingOutputDir() - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Debug Output Directory.
- readMappingOutputDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
Set outputDir. Debug Output Directory.
- ReadMappingResult(keyFileRecord, hapIdMultiset, hapIdToStatMap) - Constructor for class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin.ReadMappingResult
-
- readMappingsForLineName(configFile, lineName, readMappingMethodName, haplotypeMethodName) - Static method in class net.maizegenetics.pangenome.api.RMethods
-
- readMappingsForLineName(configFile, lineName, readMappingMethodName, haplotypeMethodName, fileGroup) - Static method in class net.maizegenetics.pangenome.api.RMethods
-
- readMappingTableInfo(configFile) - Static method in class net.maizegenetics.pangenome.api.RMethods
-
- ReadMappingUtils - Class in net.maizegenetics.pangenome.hapCalling
-
- readMethod() - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
A read method. Either a read method or a keyfile containing
mapping ids must be supplied.
If both are supplied, the keyFile will be used and
the readMethod will be ignored.
- readMethod(value) - Method in class net.maizegenetics.pangenome.hapCalling.LikelyParentsPlugin
-
Set Read Method. A read method. Either a read method
or a keyfile containing mapping ids must be supplied.
If both are supplied, the keyFile will be used and
the readMethod will be ignored.
- readMethod() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
The read method name to used for the read mapping data
stored in the DB.
- readMethod(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Read Method. The read method name to used for the
read mapping data stored in the DB.
- readMethodDescription() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
An additional description that will be stored with
the read method name, if desired.
- readMethodDescription(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Read Method Description. An additional description
that will be stored with the read method name, if desired.
- readMethodName() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
The name of the read method in the PHG DB
- readMethodName(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Read Method. The name of the read method in the
PHG DB
- readMethodName() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
The name of the read mapping method in the PHG DB
- readMethodName(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Read Mapping Method. The name of the read mapping
method in the PHG DB
- ReadMethodTablePlugin - Class in net.maizegenetics.pangenome.api
-
- ReadMethodTablePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.api.ReadMethodTablePlugin
-
- ReadNameData(queryName, refName, totalEQ, totalSNP, totalM, totalInserts, totalDeletes, editDistance, totalReadLength, totalRefLength) - Constructor for class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- readOutputFile() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
Name of Read->haplotype Mapping file.
- readOutputFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
Set Output Read-> haplotype Mapping File. Name of Read->haplotype
Mapping file.
- reads() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
File Name of the read fastq
- reads(value) - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
Set Read File. File Name of the read fastq
- RedirectStreams - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This comes from https://stackoverflow.com/questions/35706921/redirecting-the-output-of-a-process-into-the-input-of-another-process-using-proc/35709166 It is used to aid in piping output from 1 ProcessBuilder command to another.
- RedirectStreams(process1, process2) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.RedirectStreams
-
- Ref - Static variable in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- ref() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Input reference fasta file for single chromosome
- ref(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesPlugin
-
Deprecated.
Set Reference Fasta File. Input reference fasta file for single chromosome
- ref() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
-
Reference fasta File
- ref(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
-
Set Reference. Reference fasta File
- refAllele() - Method in class net.maizegenetics.pangenome.api.Variant
-
- refAlleleID() - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- refAlleleString() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- RefAltData - Class in net.maizegenetics.pangenome.hapcollapse
-
This class used when processing consensus data.
- RefAltData(variantId, chr, pos, length, refDepth, altDepth) - Constructor for class net.maizegenetics.pangenome.hapcollapse.RefAltData
-
- refChrom() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Name of reference chromsome as stored in the database. This is the chromosome whose anchors will be pulled.
- refChrom(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
Set Reference Chromosome Name. Name of reference chromsome as stored in the database. This is the chromosome whose anchors will be pulled.
- refDepth() - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- reference() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Input Reference Fasta
- reference(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin
-
Set Ref. Input Reference Fasta
- reference() - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
File Name of the reference fasta
- reference(value) - Method in class net.maizegenetics.pangenome.hapCalling.FilterFastqUsingBAMPlugin
-
Set Ref File. File Name of the reference fasta
- reference() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Input Reference Fasta
- reference(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
Set Ref. Input Reference Fasta
- reference() - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Input Reference Fasta
- reference(value) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
Set Ref. Input Reference Fasta
- reference() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
Input Reference Fasta
- reference(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin
-
Set Reference Fasta. Input Reference Fasta
- reference() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Input Reference Fasta
- reference(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Set Reference Fasta. Input Reference Fasta
- referenceFasta() - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
Reference Genome File for aligning against
- referenceFasta(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateValidIntervalsFilePlugin
-
Set Reference Genome File. Reference Genome File for
aligning against
- referenceFile() - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
Input Reference used to create the gvcf
- referenceFile(value) - Method in class net.maizegenetics.pangenome.hapcollapse.GVCFTyperPlugin
-
Deprecated.
Set Reference Fasta Sequence. Input Reference used to create the gvcf
- referenceFile() - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
-
Deprecated.
Reference Input file
- referenceFile(value) - Method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin
-
Deprecated.
Set Reference File. Reference Input file
- referenceFileName() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Reference file name in case you want to index on the fly
- referenceFileName(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Set Ref File Name. Reference file name in case you want to index on the fly
- referenceGenome() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
The reference genome fasta.
- referenceGenome(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Ref Genome. The reference genome fasta.
- referenceName() - Method in class net.maizegenetics.pangenome.api.ReferenceRange
-
Reference genome (B73, CML247, EP1, etc) from which the reference range originates
- referenceRange() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
Object containing the range of genomic coordinate values associated with a given HaplotypeNode and other details associated with that range of values. These values correspond to the reference genome being used (Generally B73 in Maize).
- referenceRange() - Method in class net.maizegenetics.pangenome.api.HaplotypeSequence
-
Reference Range in (alternative)reference genome
- ReferenceRange - Class in net.maizegenetics.pangenome.api
-
- ReferenceRange(referenceName, chromosome, start, end, id) - Constructor for class net.maizegenetics.pangenome.api.ReferenceRange
-
- ReferenceRange(referenceName, chromosome, start, end, id, method) - Constructor for class net.maizegenetics.pangenome.api.ReferenceRange
-
- ReferenceRange(referenceName, chromosome, start, end, id, methods) - Constructor for class net.maizegenetics.pangenome.api.ReferenceRange
-
- ReferenceRangeEmissionProbability - Class in net.maizegenetics.pangenome.api
-
- ReferenceRangeEmissionProbability.Builder - Class in net.maizegenetics.pangenome.api
-
- ReferenceRangeEmissionProbability.METHOD - Enum in net.maizegenetics.pangenome.api
-
- referenceRangeForAllChromMap(database, refRangeMethods) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
- referenceRangeForChromMap(database, chrom) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Find all reference ranges for a particular chromosome Query pulls all reference ranges for that chrom from the reference_ranges table. The assembly should be processed against all defined reference ranges.
- referenceRangeList() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
- referenceRangeMap(database) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Retrieves all ReferenceRange instances
- referenceRanges(database) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Retrieves all ReferenceRange instances with specified genome interval version name.
- referenceRanges() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
- referenceRanges(database, methods, methodTable) - Static method in class net.maizegenetics.pangenome.api.HaplotypeGraphStream
-
This retrieves the reference ranges matching the haplotype method / range group method pairs specified.
- referenceRanges(graph) - Static method in class net.maizegenetics.pangenome.api.RMethods
-
- referenceRangeStream() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns stream of reference ranges for entire graph.
- referenceRangeStream(chr) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns stream of reference ranges for given chromosome.
- ReferenceRangeSummaryPlugin - Class in net.maizegenetics.pangenome.api
-
- ReferenceRangeSummaryPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.api.ReferenceRangeSummaryPlugin
-
- ReferenceRangeTransitionProbability - Class in net.maizegenetics.pangenome.api
-
- ReferenceRangeTransitionProbability(anchorNodeList, hapGraph, minTransitionProb) - Constructor for class net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
-
- referenceSequence() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Reference Genome Sequence to use to extract the fasta
- referenceSequence(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Reference Genome Sequence. Reference Genome Sequence to use to extract the fasta
- refFasta() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Full path to reference fasta file, docker specific
path if running in a docker
- refFasta(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Set Reference Fasta File. Full path to reference fasta
file, docker specific path if running in a docker
- refFasta() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Input reference fasta file
- refFasta(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Set Reference Fasta File. Input reference fasta file
- refFile() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
Fasta file containing reference genome
- refFile(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
Set Ref Genome File. Fasta file containing reference genome
- refFile() - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
Reference File used to create the GVCFs.
- refFile(value) - Method in class net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin
-
Set Ref File. Reference File used to create the GVCFs.
- refGeneInsert() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Proportion of gene that will get an insertion
- refGeneInsert(value) - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Set Proportion of gene that will get an insertion
- refGenome() - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
Referemce Genome File for aligning against
- refGenome(value) - Method in class net.maizegenetics.pangenome.db_loading.AddRefRangeAsAssemblyPlugin
-
Set Reference Genome File. Referemce Genome File for aligning against
- refGenome() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Reference Genome File for aligning against
- refGenome(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Set Reference Genome File. Reference Genome File for
aligning against
- refGenome() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
Reference Genome.
- refGenome(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
Set Reference Genome. Reference Genome.
- refGenome() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Reference Genome.
- refGenome(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Set Reference Genome. Reference Genome.
- refGenomeDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- refGenomeDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- refGenomeFile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- refGenomeName - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- refGenomePath - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- refGenomePathDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- refilterCoordsFile(outputDeltaFilePrefix, coordsDelta, coordsDelta1, coordsGNoEmbedded, chrom, scoreThreshold) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Takes a mummer delta file filtered via the -1 option, determines which entries to keep. From the remaining, it removes embedded entries.
- refilterCoordsFileMinusG(outputDeltaFilePrefix, coordsDelta, coordsDeltaG, coordsGNoEmbedded, chrom) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
This method post-processes the filtered and original coords file when the mummer coords file came from a delta filtered with the -G option. It will 1. create a list of entries to add back based on groups of ascending/descending entries of at least 3 adjacent alignments whose distance from each other is less than a specified amount 2. adds the entries above (in a sorted manner) to the filtered coords list
- refInterGeneDelete() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Proportion of the reference inter-gene sequence to delete
- refInterGeneDelete(value) - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Set Proportion of InterGene Deleted. Proportion of the reference inter-gene sequence to delete
- refInterGeneDup() - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Proportion of the refererence inter-gene sequence to duplicate
- refInterGeneDup(value) - Method in class net.maizegenetics.pangenome.smallseq.CreateSmallGenomesPlugin
-
Set Proportion of InterGene Duplicate. Proportion of the refererence inter-gene sequence to duplicate
- refLen() - Method in class net.maizegenetics.pangenome.db_loading.VariantMappingData
-
- refLineName - Variable in class net.maizegenetics.pangenome.pipelineTests.RefRangeVectors
-
- refLoadDataFile - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- refLoadDataFileDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- refLoadDataFileName - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- refMaxAlignCov() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
anchorwave proali parameter R, indicating reference
genome maximum alignment coverage .
- refMaxAlignCov(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Set Ref Max Align Cov. anchorwave proali parameter
R, indicating reference genome maximum alignment coverage
.
- refName() - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
Name of file containing reference genes
- refName(value) - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
Set Ref File Name. Name of file containing reference
genes
- refPath() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
Path where reference fastas live
- refPath(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AlterNucmerFirstLinePlugin
-
Set Reference Path. Path where reference fastas live
- RefRangeData(chrom, start, end) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.RefRangeData
-
- refRangeFile() - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
File containing reference range information: csv with
columns ref_range_id, chrom,range_start,range_end
- refRangeFile(value) - Method in class net.maizegenetics.pangenome.db_loading.HaplotypeGeneMetricsPlugin
-
Set Ref Range File. File containing reference range
information: csv with columns ref_range_id, chrom,range_start,range_end
- refRangeFile() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
The name of the file containing the reference ranges to keep.
- refRangeFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Ref Range File. The name of the file containing the reference ranges to keep.
- refRangeFile() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
The name of the file containing the reference ranges to keep.
- refRangeFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Set Ref Range File. The name of the file containing the reference ranges to keep.
- refRangeFile() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
The name of the file containing the reference ranges to keep.
- refRangeFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Set Ref Range File. The name of the file containing the reference ranges to keep.
- refRangeForSNPFile() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
Reference Range file used to further subset the paths
for only specified regions of the genome.
- refRangeForSNPFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFHaplotypesPlugin
-
Set Reference Range File. Reference Range file used
to further subset the paths for only specified regions
of the genome.
- refRangeForSNPFile() - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Reference Range file used to further subset the paths
for only specified regions of the genome.
- refRangeForSNPFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin
-
Set Reference Range File. Reference Range file used
to further subset the paths for only specified regions
of the genome.
- refRangeId - Variable in class net.maizegenetics.pangenome.pipelineTests.RefRangeVectors
-
- refRangeIds - Variable in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataVectors
-
- RefrangeInfo(chr, start, end) - Constructor for class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin.RefrangeInfo
-
- refRangeMethod() - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
-
Comma separated list of reference Range methods needed to create a bed file. Generally you will want to pull down refRegionGroup
- refRangeMethod(value) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalBedFilesPlugin
-
Set Ref Range Methods. Comma separated list of reference Range methods needed to create a bed file. Generally you will want to pull down refRegionGroup
- refRangeMethods() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
Comma separated list of names given to identify conserved
vs non-conserved methods.
This is the group name from the bed file used to load
the reference ranges.
The list must contain exactly 2 names, for example:
genic,intergenic or refRegionGroup,refInterRegionGroup.
- refRangeMethods(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyConsensusMetricPlugin
-
Set Ref Range Methods. Comma separated list of names
given to identify conserved vs non-conserved methods.
This is the group name from the bed file used to load
the reference ranges.
The list must contain exactly 2 names, for example:
genic,intergenic or refRegionGroup,refInterRegionGroup.
- refRanges() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
Reference range list to remove from graph
- refRanges(value) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
Set Reference Ranges. Reference range list to remove from graph
- refRangesForChrom(dbConn, chrom) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.Mummer4DoonerBZStats
-
- refRangesForChrom(dbConn, chrom) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
- RefRangeStats(refRangeId, numReads, totalReadBps, totalAlignedBps, totalNM, totalSClip, totalHClip, totalEQ, totalX, totalI, totalD) - Constructor for class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- RefRangeVectors - Class in net.maizegenetics.pangenome.pipelineTests
-
This class creates a range of vectors holding data for PHG ReferenceRange objects
- RefRangeVectors(refRangeIds, chromosomes, startPos, endPos, refLineName, numberOfNodes) - Constructor for class net.maizegenetics.pangenome.pipelineTests.RefRangeVectors
-
- RefRangeWrapper - Class in net.maizegenetics.pangenome.hapCalling
-
Need a ReferenceRange Wrapper function as the Current ReferenceRange is not serializable due to the Chromosome object.
- RefRangeWrapper(myReferenceName, myChromosome, myStart, myEnd, myID, myMethods) - Constructor for class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
Need a ReferenceRange Wrapper function as the Current ReferenceRange is not serializable due to the Chromosome object.
- refServerDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- refServerPath() - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
String that contains a server and file path where the
reference genome will be stored for future access.
This ia a more permanent location, not where the genome
file lives for procssing via this plugin.
- refServerPath(value) - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
Set Reference Server Path. String that contains a server
and file path where the reference genome will be stored
for future access. This ia a more permanent location,
not where the genome file lives for procssing via this
plugin.
- refVersion() - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
Name of reference version as stored in the DB table genome_inteval_versions
- refVersion(value) - Method in class net.maizegenetics.pangenome.hapCalling.ExportHaplotypePathToFilePlugin
-
Set Ref Version. Name of reference version as stored in the DB table genome_inteval_versions
- REGION_REFERENCE_RANGE_GROUP - Static variable in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
- RegionHaplotypeCount(start, end, count, type) - Constructor for class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- RegionInputData(start, end, type, variantContextMap) - Constructor for class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- removeAdapter() - Method in class net.maizegenetics.pangenome.hapCalling.FastqcolToFastaPlugin
-
Whether to remove Illumina adapters
- removeEqualCounts() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Any range for which all haplotypes have the same number
of read counts will not be included in the path.
- removeEqualCounts(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Remove Equal. Any range for which all haplotypes
have the same number of read counts will not be included
in the path.
- removeExtraRangeAlignments(entry, hapIdToRangeMap, maxRefRangeError) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin
-
Simple function to go through the records grouped by range and remove any suboptimal alignments.
- removeExtraRefRangeHits(currentMapping, hapIdToRangeMap, maxRefRangeError) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to remove any reads which hit more than one reference range ambiguously.
- removeHaplotypeCaller(taxonName) - Static method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
-
Deprecated.
Simple method to remove the _Haplotype_Caller from the taxon name
- removeIndels(baseAlign) - Static method in class net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils
-
Deprecated.
Method to Remove indels from the GenotypeTable. Basically if it has a + or - in any of the calls, we filter out.
- removeLastToken() - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
If set to true, this will remove the last token from
the file names.
- removeLastToken(value) - Method in class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
Set Remove Last Token From FileName. If set to true,
this will remove the last token from the file names.
- removeLongNs(anchorSequence) - Static method in class net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
-
- RemoveLongRunNs - Class in net.maizegenetics.pangenome.multiSequenceAlignment
-
Simple test utility(script) which will remove Ns from a list of files TODO Refractor out the methods to be more object oriented Created by zrm22 on 6/7/17.
- removeRangesWithEqualCounts() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Ranges with equal read counts for all haplotypes should
be removed from the graph. Defaults to true but will
be always be false if minReads = 0.
- removeRangesWithEqualCounts(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Remove Equal. Ranges with equal read counts for
all haplotypes should be removed from the graph. Defaults
to true but will be always be false if minReads = 0.
- removeRangesWithEqualCounts(remove) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- removeRangesWithEqualCounts() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Ranges with equal read counts for all haplotypes should be removed from the graph. Defaults to true but will be always be false if minReads = 0.
- removeRangesWithEqualCounts(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Remove Equal. Ranges with equal read counts for all haplotypes should be removed from the graph. Defaults to true but will be always be false if minReads = 0.
- removeRefBlocks(variantInfos) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- removeRefRanges(graph, minPercentTaxa) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Removes reference ranges from given graph that represent less than given minimum percent of total taxa.
- removeRefRanges(graph, minCountTaxa) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Removes reference ranges from given graph that represent less than given minimum number of taxa.
- removeRefRanges(graph, ranges) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Removes specified reference ranges from graph.
- replaceNsWithMajor() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Boolean flag to replace any N calls with a Major Homozygous Diploid Value
- replaceNsWithMajor(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Replace N calls with Major Allele. Boolean flag to replace any N calls with a Major Homozygous Diploid Value
- reportFile - Static variable in class net.maizegenetics.pangenome.hapcollapse.QualityReportAnchorsToHaplotypes
-
- requiredTaxaList() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Optional list of taxa required to have haplotypes.
Any reference range that does not have a haplotype
for one of these taxa will not be used for path finding.
This can be a comma separated list of taxa (no spaces
unless surrounded by quotes), file (.txt) with list
of taxa names to include, or a taxa list file (.json
or .json.gz). By default, all taxa will be included.
- requiredTaxaList(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Required Taxa. Optional list of taxa required to
be have haplotypes. Any reference range that does not
have a haplotype for one of these taxa will not be
used for path finding. This can be a comma separated
list of taxa (no spaces unless surrounded by quotes),
file (.txt) with list of taxa names to include, or
a taxa list file (.json or .json.gz). By default, all
taxa will be included.
- resetBaseDirectory(baseDirectory) - Static method in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- resizeCoords(coordFile, chromosome) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Test method to resize the coordinate files so they are not overlapping
- resizeRefBlock(vc, refSequence, positionToSplit, isStart) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Method which will take a variant Context which needs to be split and will output 2 new variants while updating ASM_* annotations. Depending on if the splitting position is a start or end or if the assembly is increasing or decreasing, it will have to handle things differently.
- ResizeRefBlockPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- ResizeRefBlockPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
-
- ResizeRefBlockPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
-
- ResultChannelData(IdToRefRangeMap, vcList, fastaInfo) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.ResultChannelData
-
Deprecated.
- resultsfile - Static variable in class net.maizegenetics.pangenome.pipelineTests.ContrastHaplotypeAndAssemblySequence
-
- resultsfile - Static variable in class net.maizegenetics.pangenome.pipelineTests.EvaluateHaplotypeFastaInKnownIBDRegions
-
- RetrieveGenomeFileDataPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
This plugin queries the PHG genome_file_data table and
returns a tab-delimited file with data for the specified
file types.
- RetrieveGenomeFileDataPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
This plugin queries the PHG genome_file_data table and
returns a tab-delimited file with data for the specified
file types.
- RetrieveGenomeFileDataPlugin() - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
This plugin queries the PHG genome_file_data table and
returns a tab-delimited file with data for the specified
file types.
- RetrieveGenomeFileDataPluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- revCompliment() - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Create Kmers on both strands. If true, this will reverse
compliment each haplotype node's sequence and will
create kmers for both.
- revCompliment(value) - Method in class net.maizegenetics.pangenome.hapCalling.IndexKmerByHammingPlugin
-
Deprecated.
Set Reverse Compliment. Create Kmers on both strands.
If true, this will reverse compliment each haplotype
node's sequence and will create kmers for both.
- reverseCompliment(seq) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
- rightEdges(node) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns List of Right HaplotypeEdges for given HaplotypeNode
- rightHapNode() - Method in class net.maizegenetics.pangenome.api.HaplotypeEdge
-
HaplotypeNode to the right of the current edge
- rightTrimCount() - Method in class net.maizegenetics.pangenome.trimAnchors.AnchorInfo
-
- RMethods - Class in net.maizegenetics.pangenome.api
-
The purpose of this class is hold static methods that generate results that can be used by R
- RMethods.DataFrameVectors - Class in net.maizegenetics.pangenome.api
-
A data class holding columnNames, rowNames, and a dataVectors List as public fields in a format that can be easily used by rJava to create R objects
- RMethods.MatrixWithNames - Class in net.maizegenetics.pangenome.api
-
A data class holding columnNames, rowNames, and a matrix List as public fields in a format that can be easily used by rJava to create R objects. It is expected that the matrix will be a 2-D primitive Java array of some type that is converted correctly by rJava.
- romanToDecimal(romanNumber) - Static method in class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- rowNames - Variable in class net.maizegenetics.pangenome.api.RMethods.DataFrameVectors
-
- rowNames - Variable in class net.maizegenetics.pangenome.api.RMethods.MatrixWithNames
-
- RPHGMethodsKotlin - Class in net.maizegenetics.pangenome.api
-
Class for holding static Kotlin methods to be used by the rPHG package.
The intention for this class is to:
- RPHGMethodsKotlin() - Constructor for class net.maizegenetics.pangenome.api.RPHGMethodsKotlin
-
Class for holding static Kotlin methods to be used by the rPHG package.
The intention for this class is to:
- RPHGMethodsKotlin.HaplotypeSequences - Class in net.maizegenetics.pangenome.api
-
Data class for storing haplotype ID / sequence strings
- run() - Method in class net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
-
- run(listOfFiles, outputDirectory, outputListOfFiles) - Method in class net.maizegenetics.pangenome.multiSequenceAlignment.RemoveLongRunNs
-
Setup the run of the tool and start it exporting files.
- run(listOfFiles, numberOfScripts, outputDirectory) - Method in class net.maizegenetics.pangenome.multiSequenceAlignment.SplitMafftRun
-
- run2() - Method in class net.maizegenetics.pangenome.multiSequenceAlignment.ComputeNDistribution
-
- runAnchorWaveMultiThread(refFasta, colsAndData, cdsFasta, gffFile, refSamOutFile) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
- runAnchorwaveProali(gffFile, refFasta, asmFasta, cdsFasta, refSam, asmSam) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
- runCollapsePipeline(graph, referenceFasta) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
This method will loop through each reference range in the graph and will: 1. Merge all the gvcf records for a given haplotype method: 2. Cluster the haplotypes together into groups Then when done with all reference ranges, load the exported gvcfs and fastas to the db. This is the main function that processes each reference range in the graph
- runConsensusPipeline(graph, referenceFasta) - Method in class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
This method will loop through each reference range in the graph and will: 1. Merge the List of variant/ref data for a given haplotype method: 2. Cluster the haplotypes together into groups Then when done with all reference ranges, load data for each cluster to the db. This is the main function that processes each reference range in the graph
- runDeltaFilter(deltaFilePrefix, outputDir, mummer4Path) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Call mummer4 delta-filter method with parameter: -g 1-to-1 global alignment not allowing rearrangements NOTE: the -g option filters out many alignments, including inversions. Some of these will be added back when the "refilterCoords" method is run later.
- runGraphFastqToMapping(graph) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
This function will run the SAM -> ReadMapping File portion of the pipeline and will write to the DB.
- runGraphlessFastqToMapping() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
This function will run the Fastq -> ReadMapping File portion of the pipeline without needing DB access or a graph input.
- runGraphlessSamToMapping() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
This function will run the SAM -> ReadMapping File portion of the pipeline without needing DB access or a graph input.
- runGraphSamToMapping(graph) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
This function will run the SAM -> ReadMapping File portion of the pipeline and will write to the DB.
- RunGVCFTyper - Class in net.maizegenetics.pangenome.hapcollapse
-
Simple class to run the GVCFTyperPlugin until it gets integrated into TASSEL proper. Will be deleted once the plugin is in TASSEL as it can run on run_pipeline.sh. Created by zrm22 on 8/2/17.
- RunHapCollapsePipelinePlugin - Class in net.maizegenetics.pangenome.hapcollapse
-
Deprecated.
- RunHapCollapsePipelinePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapcollapse.RunHapCollapsePipelinePlugin
-
Deprecated.
- RunHapConsensusPipelinePlugin - Class in net.maizegenetics.pangenome.hapcollapse
-
This plugin creates consensus haplotypes. It processes each reference range in a separate thread using Java Futures. Data is written to the database via a single thread. Simple plugin to run the full Haplotype Collapse plugin. Will do the following steps: Steps: 1. Loop through each reference range in the graph: 1.a Extract the HaplotypeNodes with the VariantInfo data. 1.b Cluster haplotypes based on the FIndHaplotypeClustersPlugin and a genotype table containing only variantId data for sites with SNPs. 1.c Export clustered GenotypeTables 1.d Determine allele calls 2. For consensus haplotype created, upload to the database. based on RunHapCollapsePipelinePlugin NOTE: upgma is no longer supported, but may be added again later. 07/25/22
- RunHapConsensusPipelinePlugin() - Constructor for class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
- RunHapConsensusPipelinePlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
- RunHapConsensusPipelinePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin
-
- RunHapConsensusPipelinePlugin.CLUSTERING_MODE - Enum in net.maizegenetics.pangenome.hapcollapse
-
- RunHapConsensusPipelinePlugin.RunMergeAndCluster - Class in net.maizegenetics.pangenome.hapcollapse
-
This class takes a reference range, run through all the taxon with their variants List, create genotype table based on variant_id from PHG variants table. Send this genotype table through FindHaplotypeClustersPlugin Decode results from clustersPlugin into actual alleles
- RunHapConsensusPipelinePlugin.VariantInfoConsensus - Class in net.maizegenetics.pangenome.hapcollapse
-
- runLiquibaseCommand(command, outputDir) - Static method in class net.maizegenetics.pangenome.pipeline.PipelineUtilsKt
-
This returns a String indicating all went well, or that the db needs updating.
This is a String vs boolean as we will in the future add a PHG version to run
if the user does not want to update the db.
- RunMergeAndCluster(graphToMerge, dbProperties, referenceSequence) - Constructor for class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
-
- RunMergeAndCluster(graphToMerge, dbProperties, referenceSequence, rankingMap) - Constructor for class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
-
- RunMergeAndCluster() - Constructor for class net.maizegenetics.pangenome.hapcollapse.RunHapConsensusPipelinePlugin.RunMergeAndCluster
-
- runMinimapFromKeyFile(minimapLocation, keyFileName, inputFileDir, referenceFile, graph, maxRefRangeError, methodName, methodDescription, pluginParams, outputDebugReadMappingDir, outputSecondaryMappingStats, maxSecondary, inputFileFormat, fParameter, isTestMethod, updateDB, runWithoutGraph, hapIdToRefRangeMap, hapIdToLengthMap, refRangeToHapIdMap, inputFileName) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Method to run minimap2 using information provided by the Key file.
- runPlugin(input) - Method in class net.maizegenetics.pangenome.db_loading.CreateIntervalsFileFromGffPlugin
-
Convenience method to run plugin with one return object.
- runPlugin(input) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Convenience method to run plugin that returns nothing.
- runShowCoords(deltaFilePrefix, outputDir, mummer4Path) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
call mummer4 show-coords method
- runShowSNPs(deltaFilePrefix, outputDir, mummer4Path, chrom) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
This method calls show-snps using only a delta file as input
- runShowSNPsWithCat(deltaFilePrefix, coordsForShowSnps, outputDir, mummer4Path, chrom) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Fun the mummer4 show-snps entry against a delta file, using a coords file as additional input. From the command line, this would look like: cat coords_file | show-snps -T -r -H -S deltaFile
- runWithoutGraph() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
If set to true, will require the input of a JSON file
created by CreateHapIdMapsPlugin and will got require
a Graph object input.
- runWithoutGraph(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin
-
Set Run Without Graph. If set to true, will require
the input of a JSON file created by CreateHapIdMapsPlugin
and will got require a Graph object input.
- runWithoutGraph() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
If set to true, will require the input of a JSON file
created by CreateHapIdMapsPlugin and will got require
a Graph object input.
- runWithoutGraph(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set Run Without Graph. If set to true, will require
the input of a JSON file created by CreateHapIdMapsPlugin
and will got require a Graph object input.
- runWithoutGraph() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
If set to true, will require the input of a JSON file
created by CreateHapIdMapsPlugin and will got require
a Graph object input.
- runWithoutGraph(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set Run Without Graph. If set to true, will require
the input of a JSON file created by CreateHapIdMapsPlugin
and will got require a Graph object input.
- SAMAlignmentMetricsPlugin - Class in net.maizegenetics.pangenome.pipeline
-
Class to read a SAM file, then calculate and print metrics on number of matched-BPs, unmatched-BPs(SNPs),
total-aligned bps, insertions, deletions, editDistance, and the total query length. THe total refLength
is also included per user request, but this information is not terribly useful. While the query sequence
is included in the SAM file, allowing for the readLength to be determined by a seq.length call, the
reference sequence is not. The refLen is inferred from the CIGAR string: add all X,EQ,M, D values.
This means the refLen is always a total of the TotalBP-Aligned + Total_Deletions.
- SAMAlignmentMetricsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
Class to read a SAM file, then calculate and print metrics on number of matched-BPs, unmatched-BPs(SNPs),
total-aligned bps, insertions, deletions, editDistance, and the total query length. THe total refLength
is also included per user request, but this information is not terribly useful. While the query sequence
is included in the SAM file, allowing for the readLength to be determined by a seq.length call, the
reference sequence is not. The refLen is inferred from the CIGAR string: add all X,EQ,M, D values.
This means the refLen is always a total of the TotalBP-Aligned + Total_Deletions.
- SAMAlignmentMetricsPlugin() - Constructor for class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
Class to read a SAM file, then calculate and print metrics on number of matched-BPs, unmatched-BPs(SNPs),
total-aligned bps, insertions, deletions, editDistance, and the total query length. THe total refLength
is also included per user request, but this information is not terribly useful. While the query sequence
is included in the SAM file, allowing for the readLength to be determined by a seq.length call, the
reference sequence is not. The refLen is inferred from the CIGAR string: add all X,EQ,M, D values.
This means the refLen is always a total of the TotalBP-Aligned + Total_Deletions.
- SAMAlignmentMetricsPlugin.ReadNameData - Class in net.maizegenetics.pangenome.pipeline
-
- SAMAlignmentMetricsPluginKt - Class in net.maizegenetics.pangenome.pipeline
-
- samDir() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Name of the SAM/BAM dir to process.
- samDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin
-
Set SAM/BAM dir to process. Name of the SAM/BAM dir
to process.
- samDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
Set sam directory.
Path to a directory containing one or more sam/bam files.
To be recognized by this plugin, files must end with .sam or .bam
All other files in the directory will be ignored.
- samDir() - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Name of the SAM/BAM dir to process.
- samDir(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Set SAM/BAM dir to process. Name of the SAM/BAM dir
to process.
- samDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- samFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
Set sam file. Name of singular sam or bam file to process. Does not include path.
- samFile() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
Name of the SAM/BAM file to process.
- samFile(value) - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin
-
Set SAM/BAM to process. Name of the SAM/BAM file to
process.
- samFileName() - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
Name of the SAM file to process
- samFileName(value) - Method in class net.maizegenetics.pangenome.hapCalling.FastqToHapCountMinimapPlugin
-
Deprecated.
Set SAM file to process. Name of the SAM file to process
- SAMMetricsPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Plugin to extract metrics from SAM file(s) related to alignment quality.
Summary statistics are written to a tab-delimited file with one row for each input SAM file,
and include: number of mapped and unmapped reads, mean and median alignment edit distances.
it also writes one file per input SAM containing the best (lowest) edit distances for each read,
separated by new lines
- SAMMetricsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
Plugin to extract metrics from SAM file(s) related to alignment quality.
Summary statistics are written to a tab-delimited file with one row for each input SAM file,
and include: number of mapped and unmapped reads, mean and median alignment edit distances.
it also writes one file per input SAM containing the best (lowest) edit distances for each read,
separated by new lines
- SAMMetricsPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin
-
Plugin to extract metrics from SAM file(s) related to alignment quality.
Summary statistics are written to a tab-delimited file with one row for each input SAM file,
and include: number of mapped and unmapped reads, mean and median alignment edit distances.
it also writes one file per input SAM containing the best (lowest) edit distances for each read,
separated by new lines
- SAMMetricsPlugin.AlignmentSummary - Class in net.maizegenetics.pangenome.hapCalling
-
data class containing summary of alignment statstics for one file:
mappedReads: number of mapped reads
unmappedReads: number of unmapped reads
minEditDistances: list of the lowest edit distance for the alignments of each mapped read
Instead of printing the entire editDistances list, toString() calculates and prints mean and median
- SAMMetricsPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- sampleName() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Sample Name to write to the GVCF file
- sampleName(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Set Sample Name. Sample Name to write to the GVCF file
- SAMToMappingPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Plugin to take mapped reads to the pangenome in a SAM file and prepare and upload the ReadMappings to the DB.
- SAMToMappingPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.SAMToMappingPlugin
-
Plugin to take mapped reads to the pangenome in a SAM file and prepare and upload the ReadMappings to the DB.
- SAMToMappingPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- ScorePafFileByNMThresholdPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
Plugin to score a PAF file by different NM(Edit Distance) thresholds.
- ScorePafFileByNMThresholdPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.ScorePafFileByNMThresholdPlugin
-
Plugin to score a PAF file by different NM(Edit Distance) thresholds.
- ScorePafFileByNMThresholdPluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- ScoreRangesByInclusionCountsPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
Deprecated.
- ScoreRangesByInclusionCountsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin
-
Deprecated.
- scoreSamFileCountHapSetHits(samReader, hapIdToRefRangeMap, maxRefRangeError, pairedEnd, outputDebugFile, hapIdToLengthMap) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to score a sam record. This will output a Map which is the hapId Hit set.
- scriptTemplate() - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Generated Template Script for future minimap runs.
This makes it easier to run minimap on the merged
fastq files. Do not specify the script extension(.sh)
- scriptTemplate(value) - Method in class net.maizegenetics.pangenome.hapCalling.MergeFastqPlugin
-
Set Template Script Name. Generated Template Script
for future minimap runs. This makes it easier to run
minimap on the merged fastq files. Do not specify
the script extension(.sh)
- searchSeqsInFasta(shortSeqs, fastaFile, outputDir) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.FindRampSeqContigsInAssemblies
-
- secondaryMinCoverage() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
The minimum allowed Coverage count for determining
if a bp is conserved or not for the secondary wiggle
Files.
- secondaryMinCoverage(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Secondary Minimum Coverage Count. The minimum allowed
Coverage count for determining if a bp is conserved
or not for the secondary wiggle Files.
- SecondaryStats - Class in net.maizegenetics.pangenome.hapCalling
-
- SecondaryStats(AS, de, startPosition) - Constructor for class net.maizegenetics.pangenome.hapCalling.SecondaryStats
-
- secondaryWiggleDir() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Name of the directory containing the wiggle files for
determining coverage using the secondary rule.
- secondaryWiggleDir(value) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangesPlugin
-
Set Secondary wiggle directory. Name of the directory
containing the wiggle files for determining coverage
using the secondary rule.
- seqErrorRate() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Error rate used to merge alleles call hets versus homozygous
- seqErrorRate(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Sequencing error rate. Error rate used to merge alleles call hets versus homozygous
- seqHash() - Method in class net.maizegenetics.pangenome.api.HaplotypeSequence
-
Sequence hash in md5
- seqHash() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- seqLen() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- sequence() - Method in class net.maizegenetics.pangenome.api.HaplotypePath
-
Sequence from nodes comprising this path.
- sequence() - Method in class net.maizegenetics.pangenome.api.HaplotypeSequence
-
String representation of this nucleotide sequence
- sequence() - Method in class net.maizegenetics.pangenome.db_loading.AnchorDataPHG
-
- sequence - Variable in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataVectors
-
- sequenceForRegion(startPos, endPos, vcIter, refSequence) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function that generates sequence from
vcIter, a list of VariantContexts, for the region
from
startPos to
endPos.
- sequenceOutDir() - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Output Directory For storing the sequence files
- sequenceOutDir(value) - Method in class net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin
-
Deprecated.
Set Sequence Output Directory. Output Directory For storing the sequence files
- setAlleleDepths(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setAltAllele(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setAS(p) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- setAsmChrom(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setAsmEnd(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setAsmEndPos(position) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- setAsmStart(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setAsmStartPos(position) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- setAsmStrand(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setChr(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setClient(p) - Method in class net.maizegenetics.pangenome.io.SFTPConnection
-
- setCount(p) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- setCurrentEmissionProbabilities(p) - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- setCurrentNode(p) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
- setCurrentRefRangeIndex(p) - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- setDe(p) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- setEndPos(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setGenotype(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setMinProbability(p) - Method in class net.maizegenetics.pangenome.api.HaplotypeEmissionProbability
-
- setMultiset(p) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdMultiset
-
- setMyPathMethod(p) - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
- setMyPathMethod(p) - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
- setMyRefSequence(p) - Method in class net.maizegenetics.pangenome.db_loading.LoadAllIntervalsToPHGdbPlugin
-
- setMyTaxaList(p) - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
- setMyTaxaList(p) - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin
-
- setNM(p) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- setNode(anchor) - Method in class net.maizegenetics.pangenome.api.ReferenceRangeTransitionProbability
-
- setNode(node) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
sets the current reference range
- setNodePairList(p) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
- setNsToMax(originalDM) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
Function to create a new DistanceMatrix setting NaNs to the maximum value in both its row and column.
- setNumReads(p) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- setPositionToRefAndAltIdsMap(p) - Method in class net.maizegenetics.pangenome.hapCalling.PositionToRefAndAltHaplotypes
-
- setPreviousNodePairList(p) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbability
-
- setRefAllele(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setRefEndPos(position) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- setRefStartPos(position) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- setScore(score) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- setStartPos(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- setStartPositions(p) - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- setStateProbability(probTrueState) - Method in class net.maizegenetics.pangenome.hapCalling.ViterbiForDiploidPath
-
- setStrand(strand) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.PairedSimilarFragment
-
- setTotalAlignedBps(p) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- setTotalD(p) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- setTotalEQ(p) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- setTotalHClip(p) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- setTotalI(p) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- setTotalNM(p) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- setTotalReadBps(p) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- setTotalSClip(p) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- setTotalX(p) - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- setupChromLengthLookup() - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Simple method to setup the chromosome length lookup map to be used for the GenomeSequence methods
- setupIndelVariants(coordinates, refSequence, asmSequence) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Method to fill in the unmapped regions coming from nucmer. This method will create multi-bp indels between the mapped regions which can then be added to the SNP list for processing into Variants.
- setupMinimapRun(minimapLocation, referenceFile, firstFastq, secondFastq, maxSecondary, fParameter) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function that sets up the paired or single end minimap commands and builds the SamReader
- setupWholeGenomeIndexMap() - Method in class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence
-
Method to setup the RangeMap containing the start and End position of each chromosome in order Uses a new collect method which collects the stream into a RangeMap.
- setVariant(p) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- SFTPConnection - Class in net.maizegenetics.pangenome.io
-
Simple SFTPConnection class wrapper. This allows you to see what files are at the remote directory and to download and upload files to the remote server.
- SFTPConnection() - Constructor for class net.maizegenetics.pangenome.io.SFTPConnection
-
Simple SFTPConnection class wrapper. This allows you to see what files are at the remote directory and to download and upload files to the remote server.
- ShellScript_createLoadHaplotypes - Class in net.maizegenetics.pangenome.db_loading
-
Takes a list of fasta file, creates a chell script to load them.
- SimulatedReadsPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
- SimulatedReadsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
- simulatePairedEndReadsForTaxon(taxonName, myGraph) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
- simulateSingleReadsForTaxon(taxonName, myGraph) - Method in class net.maizegenetics.pangenome.hapCalling.SimulatedReadsPlugin
-
- SingleHapMapping - Class in net.maizegenetics.pangenome.hapCalling
-
- SingleHapMapping(readName, hapIdSet) - Constructor for class net.maizegenetics.pangenome.hapCalling.SingleHapMapping
-
- size() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- skipLiquibaseCheck() - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Should the liquibase check be skipped? Do not set to
true if running inside a Docker. Then, only set to
true if the PHG DB version is known to match the software
version.
- skipLiquibaseCheck(value) - Method in class net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
-
Set Skip Liquibase Check. Should the liquibase check
be skipped? Do not set to true if running inside a
Docker. Then, only set to true if the PHG DB version
is known to match the software version.
- skipLiquibaseCheck() - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Should the liquibase check be skipped? Do not set to
true if running inside a Docker. Then, only set to
true if the PHG DB version is known to match the software
version.
- skipLiquibaseCheck(value) - Method in class net.maizegenetics.pangenome.pipeline.PopulatePHGDBPipelinePlugin
-
Set Skip Liquibase Check. Should the liquibase check
be skipped? Do not set to true if running inside a
Docker. Then, only set to true if the PHG DB version
is known to match the software version.
- smallSeqBaseDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- smallSeqBaseRemoteGvcfDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- SmallSeqPaths - Class in net.maizegenetics.pangenome.smallseq
-
- snpPositions(nodes) - Static method in class net.maizegenetics.pangenome.api.GraphToGenotypeTable
-
- snpPositions(graph) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
-
Return sorted set of positions that are variant (SNP) positions in given graph.
- snpPositions(graph, referenceRanges) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
-
Return sorted set of positions that are variant (SNP) positions in given graph.
- SNPToReadMappingPlugin - Class in net.maizegenetics.pangenome.hapCalling
-
- SNPToReadMappingPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
- SNPToReadMappingPlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
- SNPToReadMappingPluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- sortListCreatehash() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- spansSingleRefRange(currentMapping, hapIdToRangeMap) - Static method in class net.maizegenetics.pangenome.hapCalling.Minimap2Utils
-
Function to check to see if the reads only hit one reference range
- SplitASMContigsByLengthPlugin - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
Plugin to split each contig in an assembly fasta into chunks. By Default 20kbp chunks are created.
Any contig less than 20kbp will be unchanged and written to the file denoted by outputFile.
- SplitASMContigsByLengthPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
Plugin to split each contig in an assembly fasta into chunks. By Default 20kbp chunks are created.
Any contig less than 20kbp will be unchanged and written to the file denoted by outputFile.
- SplitASMContigsByLengthPluginKt - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
- splitCigar(cigarString) - Static method in class net.maizegenetics.pangenome.db_loading.DBLoadingUtils
-
- splitConsensusNodes() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
split consensus nodes into one node per taxon.
- splitConsensusNodes(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Split Nodes. split consensus nodes into one node
per taxon.
- splitConsensusTaxa(tList) - Static method in class net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils
-
- SplitFastaByChromPlugin - Class in net.maizegenetics.pangenome.db_loading
-
Splits fasta by chromosome. IT assumes the id line has a chromosome of the form >1, >chr1 or >chromosome1 ALl of the above forms (case insensitive) will be written with an id line of just the number, e.g. >1 or >2 The "name" parameter is used as the basis of the name. To this name will be appended the "chr" and chrom number and .fa. For example: If the user gives "w22" as the name, the code will write files: w22chr1.fa, w22chr2.fa, etc. The isGca parameter: The assemblies starting with GCA have long text in the idLIne, with the chromosome stuck in the middle. This plugin will correctly parse these lines. OTher weird id lines are not supported and may need to be corrected manually before running through this plugin. Seems each set of assemblies that arrives has a different signature for the idline. So I keep customizing. Consider this code to the "base" plugin. On each run, if the idlines don't adhere to chr/chromosome/X or GCA, then user should run an altered version of this, or fix the idlines first.
- SplitFastaByChromPlugin() - Constructor for class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- SplitFastaByChromPlugin(parentFrame) - Constructor for class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- SplitFastaByChromPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin
-
- splitGenicReferenceRanges(inputBed, idMap, vcfdir, refGenome, minCoverage, windowSize, nThreads, resultFile, mxDiv, minLength, maxClusters) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function to split genic ranges based on haplotype number. As a by-product it prints a file with both the original
and new ranges along with their haplotype numbers. The result only contains the original intergenic ranges and the
new, subdivided genic ranges.
inputBed is a list of the input range start position, end position, and type,
where type is genic or intergenic.
vcfdir is a directory containing the gVCF files that will be used to
cluster haplotypes and calculate haplotype number. It is expected that these gVCF files will be used as the
source of haplotypes to build a PHG database. Because haplotype clustering is compute intensive the method is
multithreaded.
- splitGenomePath(genomePath) - Static method in class net.maizegenetics.pangenome.api.VariantUtils
-
This method takes a STring of the form and returns a tuple with Tuple.x=server and Tuple.y=path.
- splitIntergenicRegionsMiddleStart(chrom, start, end, maximumIntergenicGapSize, idMap, minCovCount, windowSize, maximumSearchWindow, secondaryIdMap, secondaryIdMapMinCovCount) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function to split up the intergenic regions starting from the middle bp and walking out until we hit the boundaries of the region.
- SplitKeyFilePlugin - Class in net.maizegenetics.pangenome.hapCalling
-
- SplitKeyFilePlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
- SplitKeyFilePlugin() - Constructor for class net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin
-
- SplitKeyFilePluginKt - Class in net.maizegenetics.pangenome.hapCalling
-
- SplitMafftRun - Class in net.maizegenetics.pangenome.multiSequenceAlignment
-
Simple utility to create a multithreaded script to run multiple anchors through MAFFT at a single time. This helps when running on cbsu as we can then make use of all the cores. Creates a single master script and a set of subscripts which will all run on a single thread. TODO This should be refractored to be able to run using CMD line calls from java Created by zrm22 on 6/7/17.
- splitNodes() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
If splitTaxa is true, then each taxon will be assigned
its own node in the graph prior to path finding.
- splitNodes(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Split Taxa. If splitTaxa is true, then each taxon
will be assigned its own node in the graph prior to
path finding.
- splitOverlappingCoordsEntries(sortedList, snpList, splitByRef) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing
-
Splits overlapping entries, The mummer4 coords file entries will have these tab-delimited columns: S1 E1 S2 E2 Len1 Len2 %ID refID asmID The files processed were sorted by ref-coordinates via the show-coords -r param, so S1/E1 is ref coords and S2/E2 are the assembly coordinates. When 2 entries are found to overlap, the first entry keeps its coordinates. The second will be truncated by the amount of the overlap. It is understood this may not be completely accurate as the position of indels is not considered.
- splitRefRange(variantContexts, anchorMapping, refSequence) - Static method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils
-
Method to split up the reference range by anchor mappings. Basically this method will take the variant contexts and the anchor coordinates. If a variant context is a reference block which is spanning the start or end of the anchor(should happen frequently if anchor ends are truly conserved), we need to break up the variant context into two adjacent reference blocks with the end point being the start or end of one of the variants. This will allow for easy querying of the list of Variants when attempting to load into the db.
- splitRegionFromMiddle(start, end, conservedSites, minLength) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function that splits a region in the middle, if that site is conserved and if the both subregions are at least
minLength long. Each new subregion is split in the middle again until no subregions can be split.
- splitSize() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
Maximum number of bps in an assembly chunk.
- splitSize(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.SplitASMContigsByLengthPlugin
-
Set Split Size. Maximum number of bps in an assembly
chunk.
- splitTaxa() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
split consensus nodes into one node per taxon.
- splitTaxa(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Split Taxa. split consensus nodes into one node per taxon.
- splitTransitionProb() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
When the consensus nodes are split by taxa, this is
the transition probability for moving from a node to
the next node of the same taxon. It equals 1 minus
the probability of a recombination between adjacent
nodes.
- splitTransitionProb(value) - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin
-
Set Split Prob. When the consensus nodes are split
by taxa, this is the transition probability for moving
from a node to the next node of the same taxon. It
equals 1 minus the probability of a recombination between
adjacent nodes.
- splitTransitionProb() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
When splitTaxa is true, the transition probability
for moving between nodes of the same taxon will be
set to this number.
- splitTransitionProb(value) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin
-
Set Split Probability. When splitTaxa is true, the
transition probability for moving between nodes of
the same taxon will be set to this number.
- splitTransitionProb() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon. It equals 1 minus the probability of a recombination between adjacent nodes.
- splitTransitionProb(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Split Prob. When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon. It equals 1 minus the probability of a recombination between adjacent nodes.
- splitTransitionProb() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon. It equals 1 minus the probability of a recombination between adjacent nodes.
- splitTransitionProb(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Set Split Prob. When the consensus nodes are split by taxa, this is the transition probability for moving from a node to the next node of the same taxon. It equals 1 minus the probability of a recombination between adjacent nodes.
- SplitVCFIntoIntervalsPlugin - Class in net.maizegenetics.pangenome.gvcfFiltering
-
- SplitVCFIntoIntervalsPlugin(parentFrame, isInteractive) - Constructor for class net.maizegenetics.pangenome.gvcfFiltering.SplitVCFIntoIntervalsPlugin
-
- splitW22GenomeGetChrom10() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- start() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- start() - Method in class net.maizegenetics.pangenome.api.ReferenceRange
-
Start position of reference range, inclusive
- start() - Method in class net.maizegenetics.pangenome.db_loading.GeneGFFData
-
- startNodes() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns list of HaplotypeNodes that start graph.
- startNodes(chr) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
- startPos - Variable in class net.maizegenetics.pangenome.pipelineTests.RefRangeVectors
-
- startProbabilities(numberOfNodes) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- startProbabilities(nodeList) - Static method in class net.maizegenetics.pangenome.hapCalling.FindBestDiploidPathKt
-
- storeReadMappingsInDB(multisets, fileGroupName) - Method in class net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin
-
- subsetGraph(graph, taxa) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Create graph that's a subset of the given graph which contains only nodes from the taxa list.
- sumPerChromGFFBasePairs(gffSet) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Calculates the number of BPs for each contig/chromosome in the GFF file
Overlapping positions are only counted once.
- sumPerChromNonGFFBasePairs(gffSet) - Static method in class net.maizegenetics.pangenome.annotations.GFFUtilsKt
-
Calculates the number of BPs for each contig/chromosome that were not
present in the GFF file. For example: If the chromosome is of length
2000, and there are only 850 total base pairs for that chromosome
in the GFF, then the non-represented number is 1150
- SyntenicAnchors - Class in net.maizegenetics.pangenome.processAssemblyGenomes
-
Class originally written by Baoxing Song for post-processing minimap2 alignments. It takes an input a file created by aligning with minimap2 and this command: /home/lcj34/minimap2/minimap2 -A 1 -B 1 -O 1 -E 1 -a -t 80 /workdir/lcj34/assemblies_by_chrom/p39/p39chr7.fa /workdir/lcj34/assemblies_by_chrom/b73/b73chr7anchors.fa > b37anchorsMap.sam The resulting .sam file (b37anchorsMap.sam in above query) is split to get 3 fields via grep: - refStart - asmStart - ms (DP score of the max scoring segment in the minimap alignment) longest path algorithm from here: https://www.geeksforgeeks.org/find-longest-path-directed-acyclic-graph/ The code currently has methods to run with mummer 4 coords file entries. The "score" from mummer alignments is (%id * alignment len)/100. Method getPairedSimilarFragmentsFromMummer() is written so this code may be applied to mummer4 alignment results. Similar methods may be added to create lists of PairedSimilarFragments from other aligners.
- tagCountsByTaxaFile() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
File holding the tag counts for each taxa
- tagCountsByTaxaFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
Set Tag Count By Taxa File. File holding the tag counts for each taxa
- tagNodePairCounts(tagTaxaFile, graph, outputFile) - Static method in class net.maizegenetics.pangenome.api.GraphUtils
-
- tagToHapIdMapFile() - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
tagToHapIDMappingFile
- tagToHapIdMapFile(value) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertRampSeqTagsToMapPlugin
-
Set Hap Id Mapping File. tagToHapIDMappingFile
- target() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Name of target in mummer query, this is usually the reference
- target(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MummerAnalysisMetricsPlugin
-
Deprecated.
Set Target name. Name of target in mummer query, this is usually the reference
- targetName() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
The name of the taxon to which the path will be compared.
- targetName(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Set Taxon name. The name of the taxon to which the path will be compared.
- targetTaxon(taxonName) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- targetTaxon() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
The taxon that will be used to evaluate the node list returned.
- targetTaxon(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Target. The taxon that will be used to evaluate the node list returned.
- targetTaxon() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
The taxon that will be used to evaluate the node list returned.
- targetTaxon(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Set Target. The taxon that will be used to evaluate the node list returned.
- targetTaxon() - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
Taxon which we think this path is from
- targetTaxon(value) - Method in class net.maizegenetics.pangenome.hapCalling.VerifyPathsPlugin
-
Set Target Taxon. Taxon which we think this path is
from
- taxa() - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
List of taxa for which paths will be pulled from the
database. This can be a comma separated
list of taxa (no spaces unless surrounded by quotes),
file (.txt) with list of taxa names to include, or
a taxa list file (.json or .json.gz).
- taxa(value) - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
Set Taxa. List of taxa for which paths will be pulled from
the database. This can be a comma
separated list of taxa (no spaces unless surrounded
by quotes), file (.txt) with list of taxa names to
include, or a taxa list file (.json or .json.gz).
- taxa(value) - Method in class net.maizegenetics.pangenome.annotations.PathToGFFPlugin
-
Set Taxa. Converts taxa to taxaList when the taxa comes in as a string
String should be a comma-separated list of taxa, no spaces!
- taxa() - Method in class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPlugin
-
Comma separated list of taxa. Taxa names must match
the names exsiting in the PHG database
- taxa(value) - Method in class net.maizegenetics.pangenome.db_loading.AddTaxaToTaxaGroupPlugin
-
Set Taxa List. Comma separated list of taxa. Taxa
names must match the names exsiting in the PHG database
- taxa() - Method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPlugin
-
Optional list of taxa whose paths will be deleted from
the db paths table. This can be a comma separated
list of taxa (no spaces unless surrounded by quotes),
file (.txt) with list of taxa names to include, or
a taxa list file (.json or .json.gz). Either keyFile
or taxa must be specified, but not both
- taxa(value) - Method in class net.maizegenetics.pangenome.db_updateDelete.DeletePathsPlugin
-
Set Taxa. Optional list of taxa whose paths will be
deleted from the db paths table. This can be a comma
separated list of taxa (no spaces unless surrounded
by quotes), file (.txt) with list of taxa names to
include, or a taxa list file (.json or .json.gz).
Either keyFile or taxa must be specified, but not both
- taxa() - Method in class net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin
-
Optional list of taxa to include. This can be a comma
separated list of taxa (no spaces unless surrounded
by quotes), file (.txt) with list of taxa names to
include, or a taxa list file (.json or .json.gz). By
default, all taxa will be included.
- taxa(value) - Method in class net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin
-
Set Taxa. Optional list of taxa to include. This can
be a comma separated list of taxa (no spaces unless
surrounded by quotes), file (.txt) with list of taxa
names to include, or a taxa list file (.json or .json.gz).
By default, all taxa will be included.
- taxa - Variable in class net.maizegenetics.pangenome.pipelineTests.HaplotypesDataVectors
-
- taxaFilter(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Set Taxa. A list of taxa to include in graph. Only nodes containing these taxa will be included in the graph. If no taxa list is supplied, then all taxa in the full graph will be used.
- taxaFilterList(taxaNames) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- taxaFilterList(listOfTaxa) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- taxaFilterString() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
A comma delimited list of taxa (no spaces allowed) to include in graph. Only nodes containing these taxa will be included in the graph. If no taxa list is supplied, then all taxa in the full graph will be used.
- taxaFilterString(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathPlugin
-
Deprecated.
Set Taxa. A comma delimited list of taxa (no spaces allowed) to include in graph. Only nodes containing these taxa will be included in the graph. If no taxa list is supplied, then all taxa in the full graph will be used.
- taxaFilterString() - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
A comma delimited list of taxa (no spaces allowed) to include in graph. Only nodes containing these taxa will be included in the graph. If no taxa list is supplied, then all taxa in the full graph will be used.
- taxaFilterString(value) - Method in class net.maizegenetics.pangenome.hapCalling.HapCountBestPathToTextPlugin
-
Deprecated.
Set Taxa. A comma delimited list of taxa (no spaces allowed) to include in graph. Only nodes containing these taxa will be included in the graph. If no taxa list is supplied, then all taxa in the full graph will be used.
- taxaFilterString() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
A list of taxa to include in graph. Only nodes containing these taxa will be included in the graph. If no taxa list is supplied, then all taxa in the full graph will be used.
- taxaInGraph() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Return all taxa represented in this graph.
- taxaInNodes(nodes) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
- taxaInRange(range) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns taxa represented by given reference range.
- taxaList() - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
Only gametes from these taxa will be added to the graph.
If null, then all gametes will be added for the path
method.
- taxaList(value) - Method in class net.maizegenetics.pangenome.api.AddPathsToGraphPlugin
-
Set Path Taxa List. Only gametes from these taxa will
be added to the graph. If null, then all gametes will
be added for the path method.
- taxaList() - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
Optional list of taxa to include.
- taxaList(value) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
Set Taxa List.
- taxaList(value) - Method in class net.maizegenetics.pangenome.api.FilterGraphPlugin
-
Set Taxa List. Optional list of taxa to include. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.
- taxaList() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Optional list of taxa to include. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.
- taxaList(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
Set Taxa. Optional list of taxa to include. This can be a comma separated list of taxa (no spaces unless surrounded by quotes), file (.txt) with list of taxa names to include, or a taxa list file (.json or .json.gz). By default, all taxa will be included.
- taxaList(value) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin
-
- taxaList() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
List of taxa used when the consensus sequence was created or a single taxon.
- taxaList() - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
Taxa List
- taxaList(value) - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
Set Taxa List.
- taxaList(value) - Method in class net.maizegenetics.pangenome.hapCalling.GetHapIdsForTaxonPlugin
-
- taxaList - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- taxaListMap(database) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
Retrieves all groups of taxa.
- taxon() - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
Name of taxon whose variant contexts should be pulled.
- taxon(value) - Method in class net.maizegenetics.pangenome.hapCalling.ExportVCForTaxonMethodPlugin
-
Deprecated.
Set Taxon. Name of taxon whose variant contexts should be pulled.
- taxon() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
-
Name to be assigned for the taxon
- taxon(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.ResizeRefBlockPlugin
-
Set Taxon Name. Name to be assigned for the taxon
- taxonName() - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
The name of the taxon for which the path is requested.
- taxonName(value) - Method in class net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin
-
Deprecated.
Set Taxon name. The name of the taxon for which the path is requested.
- tempFileDir - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- tempFileDirDocker - Static variable in class net.maizegenetics.pangenome.smallseq.SmallSeqPaths
-
- testChrMatch() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- testChromLength(genome) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- testDataFrame() - Static method in class net.maizegenetics.pangenome.api.RMethods
-
A test function to verify that DataFrameVectors works correctly for R
- testMafftfromJava() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- testMatrix() - Static method in class net.maizegenetics.pangenome.api.RMethods
-
A test function to verify that MatrixWithNames works correctly for R
- testObjectAssignment() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- TestPHGStuff - Class in net.maizegenetics.pangenome.db_loading
-
- testPythonLD(seq1, seq2, mode, task) - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- testSortedRange() - Static method in class net.maizegenetics.pangenome.db_loading.TestPHGStuff
-
- threadsPerRun() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Number of threads to use for each assembly processed.
This value plus the value for numRuns should be determined
based on system available threads and memory.
- threadsPerRun(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin
-
Set Threads Per Run. Number of threads to use for each
assembly processed.
This value plus the value for numRuns should be determined
based on system available threads and memory.
- toLong() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode.VariantInfo
-
- toString() - Method in class net.maizegenetics.pangenome.api.ASMVariantInfo
-
- toString() - Method in class net.maizegenetics.pangenome.api.BuildGraphFromPathsPlugin.RefrangeInfo
-
- toString() - Method in class net.maizegenetics.pangenome.api.HaplotypeEdge
-
- toString() - Method in class net.maizegenetics.pangenome.api.HaplotypeNode
-
- toString() - Method in class net.maizegenetics.pangenome.api.HaplotypePath
-
- toString() - Method in class net.maizegenetics.pangenome.api.HaplotypeSequence
-
- toString() - Method in class net.maizegenetics.pangenome.api.Method
-
- toString() - Method in class net.maizegenetics.pangenome.api.ReferenceRange
-
- toString() - Method in class net.maizegenetics.pangenome.api.ReferenceRangeEmissionProbability
-
- toString() - Method in class net.maizegenetics.pangenome.api.RPHGMethodsKotlin.HaplotypeSequences
-
- toString() - Method in class net.maizegenetics.pangenome.db_loading.GeneGFFData
-
- toString() - Method in class net.maizegenetics.pangenome.db_loading.LoadHaplotypesFromGVCFPlugin.ChromosomeGVCFRecord
-
- toString() - Method in class net.maizegenetics.pangenome.db_loading.ReadMappingDBRecord
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.BestAlignmentGroup
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingInput
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin.PathFindingResult
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingInput
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.PathFindingResult
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.FilterBAMAndGetStatsPlugin.RefRangeStats
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.GraphIdMaps
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdSetCount
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.HapIdStats
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.KeyFileUniqueRecord
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.KmerToRefRangeIdToPurgeArray
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.MultisampleBAMToMappingPlugin.ReadMappingResult
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.ReadMappingKeyFileParsed
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.RefRangeWrapper
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.SecondaryStats
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.SingleHapMapping
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.IndelDistributions
-
- toString() - Method in class net.maizegenetics.pangenome.hapCalling.VCFMetricsPlugin.VCFSummary
-
- toString() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileInput
-
- toString() - Method in class net.maizegenetics.pangenome.hapcollapse.ProfileMxdivPlugin.ProfileResult
-
- toString() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionHaplotypeCount
-
- toString() - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils.RegionInputData
-
- toString() - Method in class net.maizegenetics.pangenome.pipeline.SAMAlignmentMetricsPlugin.ReadNameData
-
- toString() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.InputChannelData
-
Deprecated.
- toString() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyHaplotypesMultiThreadPlugin.ResultChannelData
-
Deprecated.
- toString() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.InputChannelData
-
- toString() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.RefRangeData
-
- toString() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.CreateASMCoordsUpdateFilesPlugin.UpdateData
-
- toString() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.GVCFBedfileMetricPlugin.ChromosomeGVCFRecord
-
- toString() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AlignmentBlock
-
- toString() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo
-
- toString() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.MAFRecord
-
- toStringLong() - Method in class net.maizegenetics.pangenome.hapCalling.KmerMap
-
- totalNumberTaxa() - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Returns total number of taxa represented by this graph
- toTextFile(filename) - Method in class net.maizegenetics.pangenome.api.RMethods.DataFrameVectors
-
- transitionProbability(from, to) - Method in class net.maizegenetics.pangenome.hapCalling.DiploidTransitionProbabilityWithInbreeding
-
- transitionProbabilitySameTaxon(p) - Method in class net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM
-
- tree(graph) - Static method in class net.maizegenetics.pangenome.api.CreateGraphUtils
-
- tree(chr) - Method in class net.maizegenetics.pangenome.api.HaplotypeGraph
-
Creates a sorted (on keys ReferenceRanges) map to list of HaplotypeNodes for given chromosome.
- TrimGenotypeTableAnchors - Class in net.maizegenetics.pangenome.trimAnchors
-
Simple class holding utilities to trim a genotype table by identity and coverage thresholds TODO needs to be refractored and have a standardized api Created by zrm22 on 7/6/17.
- tryAdvance(action) - Method in class net.maizegenetics.pangenome.api.GraphSpliterator
-
- trySplit() - Method in class net.maizegenetics.pangenome.api.GraphSpliterator
-
- trySplitRegion(inputChannel, resultChannel, refGenome, conservedSites, mxDiv, minLength, maxClusters, p) - Method in class net.maizegenetics.pangenome.pipeline.CreateRefRangeUtils
-
Function that, when possible, splits a range into subranges at conserved sites based on the number
of haplotype clusters.
- twoGvcfs() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
The input maf was created from a diploid alignment
and should be used to create two separate gVCF files.
- twoGvcfs(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
Set Two Gvcfs. The input maf was created from a diploid
alignment and should be used to create two separate
gVCF files.
- twoOutputFiles() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin
-
- type() - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
Return information for only this type of file: options
are GVCF or FASTA. If this parameter is not present
all data will be returned
- type(value) - Method in class net.maizegenetics.pangenome.processAssemblyGenomes.RetrieveGenomeFileDataPlugin
-
Set Type. Return information for only this type of
file: options are GVCF or FASTA. If this parameter
is not present all data will be returned