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F

FASTA - enum entry in net.maizegenetics.pangenome.db_loading.DBLoadingUtils.GenomeFileType

 

fasta() - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

Fasta File to split by chromosome

fasta(String) - function in net.maizegenetics.pangenome.db_loading.SplitFastaByChromPlugin

Set Fasta File .

fastqName() - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

The name of the fastq file used to create the path.

fastqName(String) - function in net.maizegenetics.pangenome.hapCalling.PathToIgraphPlugin

Set Fastq name.

FastqToKmerCountPlugin - class in net.maizegenetics.pangenome.hapCalling

Created by zrm22 on 10/23/17.

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.

FillIndelsIntoConsensus.INDEL_MERGE_RULE - class in net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus

 

filter(HaplotypeGraph) - function in net.maizegenetics.pangenome.api.FilterGraphPlugin

 

filterAndExtractFasta(Path,String,GenomeSequence,String,Properties,boolean,String) - function in net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter

Method to filter the gvcf and extract the fasta using the config file.

filterAndExtractFasta(Path,String,GenomeSequence,String,Tuple,boolean,String) - function in net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter

Old method using a poissonProbability tuple to filter based on depth.

filterBadAlignments(GenotypeTable,double,int,double) - function in 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

filterCoordsOverlaps(String,String,String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing

Takes a mummer coords file and searches for overlaps.

filteredGraph() - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

FilterFastqUsingBAMPlugin - class in net.maizegenetics.pangenome.hapCalling

Created by zrm22 on 9/13/17.

FilterGraphPlugin - class in net.maizegenetics.pangenome.api

 

filterGVCF(String,String,Properties,boolean,String) - function in net.maizegenetics.pangenome.gvcfFiltering.ComputeMedianGVCFAndFilter

 

FilterGVCFPlugin - class in net.maizegenetics.pangenome.gvcfFiltering

 

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.

filterHaplotypeGraph(HaplotypeGraph) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

This method filters a HaplotypeGraph and sets the myGraph field of the class to the result.

filterHaplotypeGraph(HaplotypeGraph,List) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

This method filters a HaplotypeGraph and sets the myGraph field of the class to the result.

filterOnTaxa(HaplotypeGraph) - function in net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM

 

filterRefRanges() - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin

Name of ref range filter file

filterRefRanges(String) - function in net.maizegenetics.pangenome.hapCalling.ScoreRangesByInclusionCountsPlugin

Set Filter Ref Range File.

finalSnpFiltering(String,String,String) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing

 

findAlignmentsToRemove_fromMinus1Filter(List) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing

Traverse a list of mummer coords entries.

findAlignmentsToReturnFromAfterMinusGFilter(List,List) - function in net.maizegenetics.pangenome.processAssemblyGenomes.MummerScriptProcessing

Takes a list of mummer4 coordinates removed during delta-filter with -g and determines which coordinates should be returned.

findAlleleIDFromDB(String,Connection) - function in 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(Collection) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils

 

FindHaplotypeClustersPlugin - class in net.maizegenetics.pangenome.hapcollapse

Processes a multi-haplotype VCF file from one region, and identifies haplotype clusters to be collapsed in future steps into a consensus haplotype.

FindHaplotypeClustersPlugin.CLUSTER_METHOD - class in net.maizegenetics.pangenome.hapcollapse.FindHaplotypeClustersPlugin

 

findInitializationErrors() - function in com.google.protobuf.AbstractMessage

 

findInitializationErrors() - function in com.google.protobuf.AbstractMessage.Builder

 

findInitializationErrors() - function in com.google.protobuf.Haplotypegraph.GVCFIDToFileProtoOrBuilder

 

findInitializationErrors() - function in com.google.protobuf.Haplotypegraph.HaplotypeEdgeProtoOrBuilder

 

findInitializationErrors() - function in com.google.protobuf.Haplotypegraph.HaplotypeGraphProtoOrBuilder

 

findInitializationErrors() - function in com.google.protobuf.Haplotypegraph.HaplotypeNodeProtoOrBuilder

 

findInitializationErrors() - function in com.google.protobuf.Haplotypegraph.HaplotypeSequenceProtoOrBuilder

 

findInitializationErrors() - function in com.google.protobuf.Haplotypegraph.ReferenceRangeProtoOrBuilder

 

findNonOverlappingGlistPair(List,int) - function in 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.

FindProteomeGenesInAssembly - class in net.maizegenetics.pangenome.pipelineTests

NOTE: Needs to be re-worked with new db.

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.

findRefIndelStart(int,Collection) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils

Find the lowest reference start entry from a mummer snp file list of entries.

findTaxonRefCoverage(Position,int,TaxaList,Map,double,double) - function in net.maizegenetics.pangenome.hapcollapse.ConsensusProcessingUtils

 

FindTrimmedAnchorCoordinates - class in net.maizegenetics.pangenome.db_loading

NOTE: This version works on the REF only.

FindTrimmedAssemblyCoordinates - class in net.maizegenetics.pangenome.db_loading

THis file is similar to FindTrimmedAnchorCoordinates used for the reference.

findVCListForAnchor(RangeMap,Position,Position) - function in net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyProcessingUtils

 

firstReferenceRange() - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns the first reference range in this graph.

firstReferenceRange(Chromosome) - function in net.maizegenetics.pangenome.api.HaplotypeGraph

Returns the first reference range for the given chromosome.

formatMethodParamsToJSON(Map) - function in net.maizegenetics.pangenome.db_loading.DBLoadingUtils

This method takes a Map of parameterName to parameterValue, and formats them into a JSON string.

freqChartHaplotypeCollapse(String,String) - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff

 

freqHaplotypeCollapse(String,String) - function in net.maizegenetics.pangenome.db_loading.TestPHGStuff

 

fullRefCoordinateToChromCoordinate(ArrayList) - function in net.maizegenetics.dna.map.GenomeSequence

 

fullRefCoordinateToChromCoordinate(ArrayList) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence

 

fullRefCoordinateToChromCoordinate(ArrayList) - function in net.maizegenetics.pangenome.fastaExtraction.GVCFSequence

 

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