java.util.Map<K,V> mAttributes
int readStart
int referenceStart
int length
java.util.List<E> chunks
byte[] mRestOfBinaryData
int mReadLength
boolean mReadLengthValid
short mReadNameLength
boolean mReadNameLengthValid
int mCigarLength
boolean mCigarLengthValid
boolean mAttributesDecoded
boolean mCigarDecoded
boolean mBinaryDataStale
long mChunkStart
long mChunkEnd
java.util.List<E> cigarElements
int length
htsjdk.samtools.CigarOperator operator
short tag
java.lang.Object value
htsjdk.samtools.SAMBinaryTagAndValue next
htsjdk.samtools.SAMFileHeader.SortOrder sortOrder
htsjdk.samtools.SAMFileHeader.GroupOrder groupOrder
java.util.List<E> mReadGroups
java.util.List<E> mProgramRecords
java.util.Map<K,V> mReadGroupMap
java.util.Map<K,V> mProgramRecordMap
htsjdk.samtools.SAMSequenceDictionary mSequenceDictionary
java.util.List<E> mComments
java.lang.String textHeader
java.util.List<E> mValidationErrors
java.lang.String[] attributes
java.lang.String mProgramGroupId
java.lang.String mReadGroupId
java.lang.String mReadName
byte[] mReadBases
byte[] mBaseQualities
java.lang.String mReferenceName
int mAlignmentStart
int mMappingQuality
java.lang.String mCigarString
htsjdk.samtools.Cigar mCigar
java.util.List<E> mAlignmentBlocks
int mFlags
java.lang.String mMateReferenceName
int mMateAlignmentStart
int mInferredInsertSize
htsjdk.samtools.SAMBinaryTagAndValue mAttributes
java.lang.Integer mReferenceIndex
java.lang.Integer mMateReferenceIndex
java.lang.Integer mIndexingBin
htsjdk.samtools.ValidationStringency mValidationStringency
htsjdk.samtools.SAMFileHeader mHeader
java.util.Map<K,V> libraryIds
short nextLibraryId
htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy scoringStrategy
htsjdk.samtools.util.Murmur3 hasher
java.util.List<E> mSequences
java.util.Map<K,V> mSequenceMap
java.lang.String mSequenceName
int mSequenceIndex
int mSequenceLength
htsjdk.samtools.SAMValidationError.Type type
java.lang.String message
java.lang.String readName
long recordNumber
java.lang.String source
FeatureInput<T extends htsjdk.tribble.Feature> dbsnp
java.util.List<E> excludeIntervalStrings
IntervalSetRule intervalSetRule
int intervalPadding
int intervalExclusionPadding
IntervalMergingRule intervalMergingRule
TraversalParameters traversalParameters
MarkDuplicatesScoringStrategy duplicatesScoringStrategy
boolean dontMarkUnmappedMates
java.util.Set<E> accumulationLevels
java.lang.String READ_NAME_REGEX
int OPTICAL_DUPLICATE_PIXEL_DISTANCE
java.util.List<E> featureFiles
java.util.List<E> intervalStrings
java.util.List<E> readFilesNames
java.lang.String referenceFileName
java.util.List<E> variantFiles
htsjdk.samtools.ValidationStringency readValidationStringency
java.util.List<E> readIndices
java.util.List<E> featureFiles
java.util.List<E> intervalStrings
java.util.List<E> readFilesNames
java.lang.String referenceFileName
java.util.List<E> variantFiles
java.util.List<E> userEnabledReadFilterNames
java.util.List<E> userDisabledReadFilterNames
boolean disableToolDefaultReadFilters
java.util.List<E> annotationsToUse
java.util.List<E> annotationsToExclude
java.util.List<E> annotationGroupsToUse
boolean disableToolDefaultAnnotations
boolean enableAllAnnotations
SimpleInterval interval
IntervalsSkipListOneContig<T extends htsjdk.samtools.util.Locatable> variants
java.util.List<E> reads
java.util.List<E> readContext
java.lang.String name
java.util.Map<K,V> keyValueMap
java.lang.String featureFile
ReferenceBases referenceBases
java.util.List<E> variants
int shardNumber
java.lang.String contig
SimpleInterval interval
SimpleInterval paddedInterval
ShardBoundary shardBoundary
java.lang.Iterable<T> locatables
java.util.List<E> intervalsForTraversal
boolean traverseUnmapped
java.net.URI referenceUri
java.lang.String referencePath
ReferenceSource referenceSource
SerializableFunction<T,R> referenceWindowFunction
int leadingWindowBases
int trailingWindowBases
double maxAmbiguousBaseFraction
java.lang.Integer maxAmbiguousBases
ReadFilter delegateFilter
long filteredCount
VariantFilter delegateFilter
long filteredCount
int maxFragmentLength
java.util.Set<E> libraryToKeep
int minMappingQualityScore
java.lang.Integer maxMappingQualityScore
boolean pfReadOnly
boolean alignedReadsOnly
int minimumSequenceLength
boolean doNotRequireSoftclipsOnBothEnds
java.util.Set<E> PLFilterNames
java.util.Set<E> blackListedLanes
htsjdk.samtools.SAMFileHeader samHeader
ReadFilter lhs
ReadFilter rhs
java.util.List<E> blackList
java.util.Map<K,V> blacklistEntries
java.lang.String readGroup
java.lang.Integer maxReadLength
int minReadLength
java.lang.String readName
java.lang.Boolean keepOnlyReverse
java.util.Set<E> samplesToKeep
java.util.Set<E> includeIDs
java.util.Set<E> sampleTypes
ReadFilter wellFormedFilter
ContextShard shard
java.lang.String bam
ReadFilter optFilter
int lastValidPos
int firstValidPos
java.util.List<E> subshards
int currentSubShardIndex
java.util.ArrayList<E> readsSoFar
SimpleInterval currentSubShard
ContextShard nextOutput
boolean readerClosed
int readShardSize
int readShardPadding
int minAssemblyRegionSize
int maxAssemblyRegionSize
int assemblyRegionPadding
int maxReadsPerAlignmentStart
double activeProbThreshold
int maxProbPropagationDistance
boolean shuffle
java.util.List<E> intervalShards
ReferenceInputArgumentCollection referenceArguments
ReadInputArgumentCollection readArguments
IntervalArgumentCollection intervalArgumentCollection
long bamPartitionSplitSize
SequenceDictionaryValidationArgumentCollection sequenceDictionaryValidationArguments
boolean shardedOutput
java.lang.String shardedPartsDir
int numReducers
ReadsSparkSource readsSource
htsjdk.samtools.SAMFileHeader readsHeader
java.lang.String readInput
ReferenceMultiSource referenceSource
htsjdk.samtools.SAMSequenceDictionary referenceDictionary
java.util.List<E> intervals
FeatureManager features
boolean shuffle
int intervalShardPadding
int maxDepthPerSample
int readShardSize
int readShardPadding
boolean shuffle
int readShardSize
int readShardPadding
boolean shuffle
java.lang.String sparkMaster
java.util.List<E> sparkProperties
java.lang.String programName
SparkCommandLineArgumentCollection sparkArgs
java.lang.String drivingVariantFile
int variantShardSize
int variantShardPadding
boolean shuffle
htsjdk.samtools.ValidationStringency validationStringency
java.lang.String referenceURL
org.bdgenomics.adam.util.TwoBitFile twoBitFile
java.util.Map<K,V> twoBitSeqEntries
int picardToolReturnCode
ValidateVariants.ValidationType type
double MEDIAN_INSERT_SIZE
double MEDIAN_ABSOLUTE_DEVIATION
int MIN_INSERT_SIZE
int MAX_INSERT_SIZE
double MEAN_INSERT_SIZE
double STANDARD_DEVIATION
long READ_PAIRS
htsjdk.samtools.SamPairUtil.PairOrientation PAIR_ORIENTATION
int WIDTH_OF_10_PERCENT
int WIDTH_OF_20_PERCENT
int WIDTH_OF_30_PERCENT
int WIDTH_OF_40_PERCENT
int WIDTH_OF_50_PERCENT
int WIDTH_OF_60_PERCENT
int WIDTH_OF_70_PERCENT
int WIDTH_OF_80_PERCENT
int WIDTH_OF_90_PERCENT
int WIDTH_OF_99_PERCENT
java.lang.String histogramPlotFile
double maxMADTolerance
java.lang.Integer histogramWidth
float minimumPct
boolean producePlot
MetricAccumulationLevelArgumentCollection metricAccumulationLevel
InsertSizeMetricsArgumentCollection inputArgs
java.lang.String output
java.lang.String SAMPLE
java.lang.String LIBRARY
java.lang.String READ_GROUP
java.util.List<E> outputOrderedDistributors
org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector.AllReadsDistributor<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,HISTOGRAM_KEY extends java.lang.Comparable<HISTOGRAM_KEY>,ARGTYPE,UNIT_COLLECTOR extends PerUnitMetricCollector<METRIC_TYPE,HISTOGRAM_KEY,ARGTYPE>> allReadsDistributor
java.util.Map<K,V> histograms
java.lang.String sample
java.lang.String library
java.lang.String readGroup
double minimumPct
double deviations
java.lang.Integer histogramWidth
double totalInserts
boolean useOriginalQualities
boolean finalized
int TOTAL_READS
int PF_READS
int READ_LENGTH
long TOTAL_BASES
long PF_BASES
long Q20_BASES
long PF_Q20_BASES
long Q30_BASES
long PF_Q30_BASES
long Q20_EQUIVALENT_YIELD
long PF_Q20_EQUIVALENT_YIELD
boolean useOriginalQualities
int PRESERVE_QSCORES_LESS_THAN
java.lang.Boolean useOriginalBaseQualities
int quantizationLevels
java.util.List<E> staticQuantizationQuals
boolean roundDown
boolean emitOriginalQuals
double globalQScorePrior
ShardBoundary boundaries
java.lang.Iterable<T> reads
ReadsDownsampler downsampler
long readCount
long QC_failure
long duplicates
long mapped
long paired_in_sequencing
long read1
long read2
long properly_paired
long with_itself_and_mate_mapped
long singletons
long with_mate_mapped_to_a_different_chr
long with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5
java.lang.String output
HaplotypeCallerSpark.ShardingArgumentCollection shardingArgs
HaplotypeCallerArgumentCollection hcArgs
ReferenceMultiSource source
htsjdk.samtools.SAMSequenceDictionary sequenceDictionary
int readShardSize
int readShardPadding
int minAssemblyRegionSize
int maxAssemblyRegionSize
int assemblyRegionPadding
int maxReadsPerAlignmentStart
double activeProbThreshold
int maxProbPropagationDistance
java.util.List<E> inputReadCountFiles
java.io.File inputAnnotatedIntervalsFile
java.io.File outputPanelOfNormalsFile
double minimumIntervalMedianPercentile
double maximumZerosInSamplePercentage
double maximumZerosInIntervalPercentage
double extremeSampleMedianPercentile
boolean doImputeZeros
double extremeOutlierTruncationPercentile
int numEigensamplesRequested
int maximumChunkSize
double pAlt
double pActive
double cnvCoherenceLength
double classCoherenceLength
int maxCopyNumber
double meanBiasStandardDeviation
double mappingErrorRate
double globalPsiScale
double samplePsiScale
int maxBiasFactors
double mappingErrorRate
double intervalPsiScale
double samplePsiScale
double depthCorrectionTau
double logMeanBiasStandardDeviation
double initARDRelUnexplainedVariance
int numGCBins
double gcCurveStandardDeviation
GermlineDenoisingModelArgumentCollection.CopyNumberPosteriorExpectationMode copyNumberPosteriorExpectationMode
boolean enableBiasFactors
int activeClassPaddingHybridMode
double learningRate
double adamaxBeta1
double adamaxBeta2
int logEmissionSamplesPerRound
double logEmissionMedianRelError
int logEmissionSamplingRounds
int maxADVIItersFirstEpoch
int maxADVIItersSubsequentEpochs
int minTrainingEpochs
int maxTrainingEpochs
double initialTemperature
int numThermalADVIIters
int convergenceSNRAveragingWindow
double convergenceSNRTriggerThreshold
int convergenceSNRCountdownWindow
int maxCallingIters
double callerUpdateConvergenceThreshold
double callerInternalAdmixingRate
double callerExternalAdmixingRate
boolean disableSampler
boolean disableCaller
boolean disableAnnealing
java.lang.String outputFile
FeatureInput<T extends htsjdk.tribble.Feature> knownVariants
OptionalVariantInputArgumentCollection optionalVariants
java.lang.String outputFile
java.io.PrintStream outputStream
java.io.File OUTPUT_FILE
java.lang.String path
int parts
java.lang.String outputFile
java.lang.String outputFile
FeatureInput<T extends htsjdk.tribble.Feature> auxiliaryVariants
ExampleMultiMetricsArgumentCollection exampleArgs
ExampleMultiMetricsCollectorSpark exampleMultiCollector
int NUMREADS
MetricAccumulationLevelArgumentCollection metricAccumulationLevel
ExampleMultiMetricsArgumentCollection inputArgs
ExampleMultiMetricsArgumentCollection inputArgs
ExampleMultiMetricsCollector collector
ExampleMultiMetricsCollector reducedResultMetrics
htsjdk.samtools.metrics.MetricsFile<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable> metricsFile
ExampleMultiMetrics metrics
ExampleSingleMetricsArgumentCollection exampleArgs
ExampleSingleMetricsCollectorSpark exampleSingleCollector
int NUMREADS
ExampleSingleMetricsArgumentCollection args
htsjdk.samtools.metrics.MetricsFile<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable> metricsFile
java.lang.String output
java.lang.String bqsrRecalFile
ApplyBQSRArgumentCollection applyBQSRArgs
java.util.List<E> knownVariants
JoinStrategy joinStrategy
java.lang.String outputTablesPath
RecalibrationArgumentCollection bqsrArgs
int readShardSize
int readShardPadding
RecalibrationArgumentCollection bqsrArgs
RequiredReadInputArgumentCollection readArguments
IntervalArgumentCollection intervalArgumentCollection
ReferenceInputArgumentCollection referenceArguments
java.util.List<E> knownVariants
java.lang.String outputTablesPath
java.lang.String inputGCSPath
java.lang.String inputGlob
java.lang.String outputHDFSDirectory
java.lang.String outputFile
boolean showVerbose
java.util.List<E> metadata
boolean outputInsertLength
java.lang.String indexImageFile
BwaMemIndexImageCreator
. If this argument is not specified, the default behavior is to look for a
file whose name is the FASTA reference file with a .img suffix.boolean singleEndAlignment
java.lang.String output
BwaArgumentCollection bwaArgs
org.apache.logging.log4j.Logger logger
int kSize
int kmerCountThreshold
public void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
java.lang.String kmerSetPath
int kmerCountThreshold
int minIdentity
java.lang.String inputPaired
java.lang.String inputUnpaired
java.lang.String outputPaired
java.lang.String outputUnpaired
PSBwaArgumentCollection bwaArgs
java.lang.String outputPaired
java.lang.String outputUnpaired
PSFilterArgumentCollection filterArgs
PSFilterArgumentCollection filterArgs
PSBwaArgumentCollection bwaArgs
PSScoreArgumentCollection scoreArgs
java.lang.String outputPath
int readsPerPartition
int readsPerPartitionOutput
java.lang.String pairedInput
java.lang.String unpairedInput
java.lang.String outputPath
PSScoreArgumentCollection scoreArgs
int recommendedNumReducers
java.lang.String bwaImage
java.lang.String referencePath
int seedLength
int maxAlternateHits
int scoreThreshold
int bwaThreads
int bwaThreads
boolean alignedInput
java.lang.String kmerFilePath
boolean skipFilters
boolean skipPreBwaRepartition
Advanced optimization option that should be used only in the case of inputs with a high proportion of microbial reads that are not host-aligned/coordinate-sorted.
In the filter tool, the input reads are initially divided up into smaller partitions (default size is usually the size of one HDFS block, or ~64MB) that Spark works on in parallel. In samples with a low proportion of microbial reads (e.g. < 1%), the steps leading up to the host BWA alignment will whittle these partitions down to a small fraction of their original size. At that point, the distribution of reads across the partitions may be unbalanced.
For example, say the input is 256MB and Spark splits this into 4 even partitions. It is possible that, after running through the quality filters and host kmer search, there are 5% remaining in partition #1, 8% in partition #2, 2% in partition #3, and 20% in partition #4. Thus there is an imbalance of work across the partitions. To correct this, a "reparitioning" is invoked that distributes the reads evenly. Note this is especially important for host-aligned, coordinate-sorted inputs, in which unmapped reads would be concentrated in the last partitions.
If, however, the proportion of microbial reads is higher, say 30%, then the partitions are generally more balanced (except for in the aforementioned coordinate-sorted case). In this case, the time spent doing the repartitioning is usually greater than the time saved by rebalancing, and this option should be invoked.
int minReadLength
int maxAmbiguousBases
int qualPhredThresh
int readTrimThresh
int dustMask
int dustW
double dustT
int minIdentity
int hostKmerThresh
java.lang.String indexImageFile
int minSeedLength
int filterReadsPerPartition
boolean filterDuplicates
int minAdapterLength
int maxAdapterMismatches
java.lang.String filterMetricsFileUri
It also provides the following:
Note that using this option may substantially increase runtime.
java.lang.String scoresPath
java.lang.String taxonomyDatabasePath
double minIdentity
double identityMargin
For example, consider a read that aligns to two different sequences, one with identity score 0.90 and the other with 0.85. If the minimum identity score is 0.7, the best hit (with score 0.90) is counted. In addition, if the identity margin is 10%, then any additional alignments at or above 0.90 * (1 - 0.10) = 0.81 would also be counted. Therefore in this example the second alignment with score 0.85 would be counted.
boolean divideByGenomeLength
boolean notNormalizedByKingdom
java.lang.String headerWarningFile
int readsPerPartitionEstimate
java.lang.String scoreMetricsFileUri
Note that using this option may increase runtime.
java.util.List<E> baseRecalibrationKnownVariantPaths
java.lang.String output
JoinStrategy joinStrategy
RecalibrationArgumentCollection bqsrArgs
int readShardSize
int readShardPadding
ApplyBQSRUniqueArgumentCollection applyBqsrArgs
BwaArgumentCollection bwaArgs
java.lang.String output
MarkDuplicatesSparkArgumentCollection markDuplicatesSparkArgumentCollection
java.lang.String out
java.lang.String out
java.lang.String input
java.lang.String out
java.lang.String out
java.lang.String output
java.lang.String output
boolean align
java.util.List<E> baseRecalibrationKnownVariants
java.lang.String output
java.lang.String outputBam
JoinStrategy joinStrategy
MarkDuplicatesSparkArgumentCollection markDuplicatesSparkArgumentCollection
BwaArgumentCollection bwaArgs
RecalibrationArgumentCollection bqsrArgs
HaplotypeCallerSpark.ShardingArgumentCollection shardingArgs
ApplyBQSRUniqueArgumentCollection applyBqsrArgs
HaplotypeCallerArgumentCollection hcArgs
java.lang.String outputFile
java.lang.String out
java.io.File chartOutput
boolean alignedReadsOnly
boolean pfReadsOnly
InsertSizeMetricsArgumentCollection insertSizeArgs
InsertSizeMetricsCollectorSpark insertSizeCollector
boolean ASSUME_SORTED
java.lang.String outputBaseName
MetricAccumulationLevelArgumentCollection metricAccumulationLevel
java.util.List<E> userCollectors
java.util.List<E> externalCollectors
QualityYieldMetricsArgumentCollection qualityYieldArgs
QualityYieldMetricsCollectorSpark qualityYieldCollector
InsertSizeMetricsArgumentCollection inputArgs
InsertSizeMetricsCollector collector
InsertSizeMetricsCollector resultMetrics
htsjdk.samtools.metrics.MetricsFile<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable> metricsFile
java.lang.String out
java.io.File chartOutput
boolean alignedReadsOnly
boolean pfReadsOnly
java.lang.String out
java.io.File chartOutput
boolean alignedReadsOnly
boolean pfReadsOnly
boolean includeNoCalls
QualityYieldMetricsArgumentCollection args
htsjdk.samtools.metrics.MetricsFile<BEAN extends htsjdk.samtools.metrics.MetricBase,HKEY extends java.lang.Comparable> metricsFile
java.lang.Integer minAlignLength
java.lang.String truthVCF
int assemblyImpreciseEvidenceOverlapUncertainty
int impreciseVariantEvidenceThreshold
java.lang.String cnvCallsFile
int truthIntervalPadding
int maxCallableImpreciseVariantDeletionSize
boolean outputCpxResultsInHumanReadableFormat
int kSize
int maxDUSTScore
int minEvidenceMapQ
int minEvidenceMatchLength
int allowedShortFragmentOverhang
int maxTrackedFragmentLength
int highDepthCoveragePeakFactor
int highDepthCoverageFactor
int minEvidenceWeight
int minCoherentEvidenceWeight
int minKmersPerInterval
int cleanerMaxIntervals
int cleanerMinKmerCount
int cleanerMaxCopyNumber
int assemblyToMappedSizeRatioGuess
int maxFASTQSize
int exclusionIntervalPadding
boolean includeMappingLocation
boolean intervalOnlyAssembly
int externalEvidenceWeight
int externalEvidenceUncertainty
java.lang.String adapterSequence
boolean writeGFAs
boolean popVariantBubbles
boolean removeShadowedContigs
boolean expandAssemblyGraph
int zDropoff
java.lang.String alignerIndexImageFile
java.lang.String externalEvidenceFile
java.lang.String metadataFile
java.lang.String evidenceDir
java.lang.String unfilteredEvidenceDir
java.lang.String intervalFile
java.lang.String highCoverageIntervalsFile
java.lang.String qNamesMappedFile
java.lang.String kmerFile
java.lang.String qNamesAssemblyFile
java.lang.String fastqDir
java.lang.String targetLinkFile
java.lang.String exclusionIntervalsFile
java.lang.String kmersToIgnoreFile
java.lang.String crossContigsToIgnoreFile
htsjdk.samtools.SAMFileHeader.SortOrder assembliesSortOrder
org.apache.logging.log4j.Logger localLogger
StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection evidenceAndAssemblyArgs
StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection discoverStageArgs
java.lang.String outputAssemblyAlignments
java.lang.String variantsOutDir
java.lang.Boolean expInterpret
org.apache.spark.api.java.JavaSparkContext ctx
java.util.List<E> alignedAssemblyOrExcuseList
htsjdk.samtools.SAMFileHeader header
org.apache.logging.log4j.Logger localLogger
StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection discoverStageArgs
java.lang.String prefixForOutput
org.apache.logging.log4j.Logger localLogger
StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection discoverStageArgs
java.lang.String nonCanonicalChromosomeNamesFile
java.lang.String outputPrefix
boolean writeSAMFiles
org.apache.spark.api.java.JavaRDD<T> unfilteredContigAlignments
htsjdk.samtools.SAMFileHeader header
boolean splitGapped
org.apache.logging.log4j.Logger localLogger
StructuralVariationDiscoveryArgumentCollection.DiscoverVariantsFromContigsAlignmentsSparkArgumentCollection discoverStageArgs
java.lang.String nonCanonicalChromosomeNamesFile
java.lang.String complexVCF
java.lang.String derivedSimpleVCFPrefix
java.lang.String outputFile
boolean writeAsBinary
StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection params
java.lang.String outputDir
java.lang.String alignerIndexFile
int maxFastqSize
java.lang.String fastqDir
boolean writeGFAs
boolean popVariantBubbles
boolean removeShadowedContigs
boolean expandAssemblyGraph
int zDropoff
java.lang.String outputFile
int kSize
int maxDUSTScore
java.lang.String highCopyFastaFilename
StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection params
java.lang.String outputAssemblyAlignments
int minEvidenceMapQ
int minEvidenceMatchLength
int allowedShortFragmentOverhang
int maxDUSTScore
int kSize
int[] partitions
org.broadinstitute.hellbender.tools.spark.sv.utils.ExternalCommandlineProgramModule.RuntimeInfo.ReturnStatus returnStatus
java.lang.String stdoutMsg
java.lang.String stderrMsg
java.lang.String moduleName
java.lang.String readNameFile
java.lang.String outputSAM
int end
int length
org.apache.spark.broadcast.Broadcast<T> headerBcast
org.apache.spark.broadcast.Broadcast<T> referenceSequenceDictionaryBcast
RecalibrationArgumentCollection recalArgs
BaseRecalibrationEngine recalibrationEngine
java.lang.String output
java.lang.String metricsFile
MarkDuplicatesSparkArgumentCollection markDuplicatesSparkArgumentCollection
OpticalDuplicatesArgumentCollection opticalDuplicatesArgumentCollection
java.util.List<E> sets
int numSets
int capacity
int size
long[] buckets
byte[] status
ReadFilter filter
ReadTransformer transformer
java.lang.String input2
boolean printSummary
boolean throwOnDiff
byte[] bin
long[][] mat
long[][] binnedMat
boolean USE_NEW_AF_CALCULATOR
boolean ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED
java.lang.Double snpHeterozygosity
double indelHeterozygosity
double heterozygosityStandardDeviation
double STANDARD_CONFIDENCE_FOR_CALLING
int MAX_ALTERNATE_ALLELES
GenotypeCalculationArgumentCollection.MAX_GENOTYPE_COUNT
.int MAX_GENOTYPE_COUNT
GenotypeCalculationArgumentCollection.MAX_GENOTYPE_COUNT
2. the value of GenotypeCalculationArgumentCollection.MAX_ALTERNATE_ALLELES
See also GenotypeCalculationArgumentCollection.MAX_ALTERNATE_ALLELES
.java.util.List<E> inputPrior
int samplePloidy
FeatureInput<T extends htsjdk.tribble.Feature> supportVariants
int numRefIfMissing
GenotypeCalculationArgumentCollection genotypeArgs
GenotypingOutputMode genotypingOutputMode
FeatureInput<T extends htsjdk.tribble.Feature> alleles
boolean genotypeFilteredAlleles
double CONTAMINATION_FRACTION
java.io.File CONTAMINATION_FRACTION_FILE
org.apache.commons.collections4.map.DefaultedMap<K,V> sampleContamination
boolean mapHasContaminationSet
AFCalculatorImplementation requestedAlleleFrequencyCalculationModel
java.io.File exactCallsLog
OutputMode outputMode
boolean annotateAllSitesWithPLs
GenotypeLikelihoodsCalculationModel GLmodel
java.lang.Double PCR_error
boolean COMPUTE_SLOD
PairHMM.Implementation pairHMM
int MIN_BASE_QUALTY_SCORE
java.lang.Double MAX_DELETION_FRACTION
int MIN_INDEL_COUNT_FOR_GENOTYPING
double MIN_INDEL_FRACTION_PER_SAMPLE
byte INDEL_GAP_CONTINUATION_PENALTY
byte INDEL_GAP_OPEN_PENALTY
int INDEL_HAPLOTYPE_SIZE
boolean OUTPUT_DEBUG_INDEL_INFO
boolean IGNORE_SNP_ALLELES
boolean TREAT_ALL_READS_AS_SINGLE_POOL
boolean IGNORE_LANE_INFO
FeatureInput<T extends htsjdk.tribble.Feature> referenceSampleRod
java.lang.String referenceSampleName
byte minQualityScore
byte maxQualityScore
byte phredScaledPrior
double minPower
boolean confidentlyCalled
boolean shouldEmit
AssemblyRegionTrimmerArgumentCollection assemblyRegionTrimmerArgs
ReadThreadingAssemblerArgumentCollection assemblerArgs
LikelihoodEngineArgumentCollection likelihoodArgs
boolean debug
boolean useFilteredReadMapForAnnotations
java.lang.String bamOutputPath
HaplotypeBAMWriter.WriterType bamWriterType
boolean dontUseSoftClippedBases
boolean captureAssemblyFailureBAM
boolean errorCorrectReads
boolean doNotRunPhysicalPhasing
byte minBaseQualityScore
SmithWatermanAligner.Implementation smithWatermanImplementation
java.lang.String sampleNameToUse
DbsnpArgumentCollection dbsnp
java.util.List<E> comps
ReferenceConfidenceMode emitReferenceConfidence
java.util.List<E> GVCFGQBands
int indelSizeToEliminateInRefModel
boolean USE_ALLELES_TRIGGER
boolean disableOptimizations
java.lang.String keepRG
boolean justDetermineActiveRegions
boolean dontGenotype
int maxMnpDistance
ReadLikelihoodCalculationEngine.Implementation likelihoodEngineImplementation
byte BASE_QUALITY_SCORE_THRESHOLD
int gcpHMM
PairHMM.Implementation pairHMM
PairHMMLikelihoodCalculationEngine.PCRErrorModel pcrErrorModel
int phredScaledGlobalReadMismappingRate
PairHMMNativeArgumentCollection pairHMMNativeArgs
java.util.List<E> kmerSizes
boolean dontIncreaseKmerSizesForCycles
boolean allowNonUniqueKmersInRef
int numPruningSamples
boolean DEPRECATED_RecoverDanglingHeads
boolean doNotRecoverDanglingBranches
int minDanglingBranchLength
boolean consensusMode
int maxNumHaplotypesInPopulation
boolean errorCorrectKmers
int minPruneFactor
boolean debugGraphTransformations
java.lang.String graphOutput
int kmerLengthForReadErrorCorrection
int minObservationsForKmerToBeSolid
int kmerSize
org.apache.logging.log4j.Logger logger
int maxMismatchesInDanglingHead
boolean alreadyBuilt
boolean startThreadingOnlyAtExistingVertex
java.util.Map<K,V> pending
java.util.Set<E> nonUniqueKmers
java.util.Map<K,V> uniqueKmers
boolean debugGraphTransformations
byte minBaseQualityToUseInAssembly
boolean increaseCountsThroughBranches
Kmer refSource
java.lang.String tumorSample
java.lang.String normalSample
FeatureInput<T extends htsjdk.tribble.Feature> pon
boolean genotypePonSites
boolean genotypeGermlineSites
FeatureInput<T extends htsjdk.tribble.Feature> germlineResource
double afOfAllelesNotInGermlineResource
double emissionLod
FilterMutectCalls
should then filter.double initialTumorLod
double maxPopulationAlleleFrequency
int downsamplingStride
int maxSuspiciousReadsPerAlignmentStart
double normalLod
int maxMnpDistance
java.io.File tumorSegmentationTable
double log10PriorProbOfSomaticEvent
double TUMOR_LOD_THRESHOLD
double NORMAL_ARTIFACT_LOD_THRESHOLD
double maxGermlinePosterior
int numAltAllelesThreshold
int minPcrSlippageBases
double pcrSlippageRate
double pcrSlippagePValueThreshold
int minMedianMappingQuality
int minMedianBaseQuality
int maxMedianFragmentLengthDifference
int minMedianReadPosition
int maxEventsInRegion
double strandArtifactPosteriorProbThreshold
double strandArtifactAlleleFractionThreshold
java.io.File contaminationTable
double maxContaminationProbability
int uniqueAltReadCount
double alpha
double beta
int n
int maxMismatches
int minClipLength
java.util.List<E> adapterSequences
int qTrimmingThreshold
int BASE_QUALITY_THRESHOLD
QuantizationInfo quantizationInfo
RecalibrationTables recalibrationTables
StandardCovariateList covariates
htsjdk.samtools.SAMFileHeader header
int preserveQLessThan
double globalQScorePrior
boolean emitOriginalQuals
int totalCovariateCount
int specialCovariateCount
RecalDatum[] empiricalQualCovsArgs
boolean useOriginalBaseQualities
byte[] staticQuantizedMapping
CovariateKeyCache keyCache
int MASK_PHRED
int W
double T
int fromQuality
int toQuality
int windowSize
int threshAT
int threshGC
int contigIndex
int start
int stop
java.lang.String contigName
int maxCapacity
int start
int end
java.lang.String contig
double cd
double ce
int cb
byte minBaseQual
double[][][] EPSILONS
java.lang.String image
java.lang.String image
java.lang.String index
java.lang.String reference
java.lang.String file
java.util.OptionalLong line
java.util.Map<K,V> intervals
int shift
java.util.List<E> vs
java.lang.String contig
int[] reach
int reachLength
java.lang.Object[] data
int numDimensions
int[] dimensions
DownsampleType type
java.lang.Integer toCoverage
java.lang.Double toFraction
Haplotype haplotype
byte[] ref
htsjdk.samtools.util.Locatable refLoc
java.lang.String sourceNameToAdd
htsjdk.samtools.util.Locatable genomeLocation
EventMap eventMap
htsjdk.samtools.Cigar cigar
int alignmentStartHapwrtRef
double score
boolean performDownsampling
int toCoverage
java.util.Map<K,V> deciles
double center
double lower
double upper
DecileCollection deciles
java.lang.String bam
java.lang.String index
java.lang.String path
byte[] index
htsjdk.samtools.QueryInterval interval
boolean removeHeader
org.bdgenomics.formats.avro.AlignmentRecord alignmentRecord
htsjdk.samtools.SAMFileHeader header
htsjdk.samtools.SAMFileHeader header
htsjdk.samtools.SAMRecord samRecord
CovariateKeyCache keyCache
EventType[] cachedEventTypes
RecalibrationArgumentCollection recalArgs
RecalibrationTables recalTables
htsjdk.samtools.SAMFileHeader readsHeader
StandardCovariateList covariates
BAQ baq
long numReadsProcessed
boolean finalized
java.util.List<E> quantizedQuals
java.util.List<E> empiricalQualCounts
int quantizationLevels
double estimatedQReported
double empiricalQuality
long numObservations
double numMismatches
int MISMATCHES_CONTEXT_SIZE
int INDELS_CONTEXT_SIZE
int MAXIMUM_CYCLE_VALUE
byte MISMATCHES_DEFAULT_QUALITY
byte INSERTIONS_DEFAULT_QUALITY
byte DELETIONS_DEFAULT_QUALITY
byte LOW_QUAL_TAIL
int QUANTIZING_LEVELS
java.lang.String BINARY_TAG_NAME
double BAQGOP
int PRESERVE_QSCORES_LESS_THAN
boolean enableBAQ
boolean computeIndelBQSRTables
java.lang.Boolean useOriginalBaseQualities
byte defaultBaseQualities
java.lang.String DEFAULT_PLATFORM
java.lang.String FORCE_PLATFORM
java.io.File existingRecalibrationReport
int qualDimension
int eventDimension
int numReadGroups
StandardCovariateList covariates
NestedIntegerArray<T extends java.io.Serializable> readGroupTable
NestedIntegerArray<T extends java.io.Serializable> qualityScoreTable
java.util.List<E> additionalTables
java.util.List<E> allTables
java.util.Map<K,V> covariateToTable
java.util.Map<K,V> tableToCovariate
int mismatchesContextSize
int indelsContextSize
int mismatchesKeyMask
int indelsKeyMask
byte lowQualTail
int MAXIMUM_CYCLE_VALUE
java.util.Map<K,V> readGroupLookupTable
java.util.Map<K,V> readGroupReverseLookupTable
ReadGroupCovariate readGroupCovariate
QualityScoreCovariate qualityScoreCovariate
java.util.List<E> additionalCovariates
java.util.List<E> allCovariates
java.util.Map<K,V> indexByClass
byte[] bases
SimpleInterval interval
SimpleInterval interval
boolean snp
boolean indel
htsjdk.variant.variantcontext.VariantContext variantContext
java.lang.String sample
java.nio.file.Path source
java.lang.String info
java.util.regex.Pattern delimiterPattern
java.lang.String delimiterString