PairedRead
reads
Parameters
jointcaller
ParsedLoci
parsing
ParsedLociRange
parsing
ParsedLociRanges
parsing
PartitionIndex
LociPartitioner
PartitionLoci
commands
PartitionLociArgs
commands
PartitionReads
commands
PartitionReadsArgs
commands
PartitionedReads
readsets
PartitionedRegions
rdd
PartitionedRegionsArgs
rdd
Path
AffineGapPenaltyAlignment DeBruijnGraph
PerSample
readsets
Pileup
pileup
PileupElement
pileup
PileupFlatMapUtils
distributed
PileupStats
pileup_summarization
Position
reference
Presence
SomaticGenotypePolicy
parallelism
UniformPartitionerArgs
parameters
InsufficientNormal StrandBias TooManyCallsAtSite MultiSampleSingleAlleleEvidence
parents
DeBruijnGraph
parseFilters
ReadFilterArgs
parsing
loci
partition
CappedRegionsPartitioner LociPartitioner MicroRegionPartitioner UniformPartitioner
partitionContigStats
LociPartitioning
partitionDepths
CoverageRDD
partitionRangesStats
LociPartitioning
partitionSets
LociPartitioning
partitionSizeStats
LociPartitioning
partitionedReadsPathOpt
PartitionedRegionsArgs
partitioning
loci
partitioningAccuracy
MicroRegionPartitionerArgs
passedVendorQualityChecks
InputFilters
path
Input Input
paths
Arguments Base SingleSampleArgs TumorNormalReadsArgs
perNormalSampleGermlinePosteriors
MultiSampleSingleAlleleEvidence
perTumorDnaSampleSomaticPosteriors
MultiSampleSingleAlleleEvidence
perTumorDnaSampleTopMixtures
MultiSampleSingleAlleleEvidence
perTumorRnaSampleSomaticPosteriors
MultiSampleSingleAlleleEvidence
perTumorRnaSampleTopMixtures
MultiSampleSingleAlleleEvidence
phredScaledLikelihood
AlleleEvidence
phredScaledSomaticLikelihood
CalledSomaticAllele
phredValue
StrandBias
pileup
guacamole
pileupFlatMapMultipleSamples
PileupFlatMapUtils
pileupFlatMapOneSample
PileupFlatMapUtils
pileupFlatMapTwoSamples
PileupFlatMapUtils
pileup_summarization
jointcaller
pileupsToAlleleCounts
Caller
pooledGermlinePosteriors
MultiSampleSingleAlleleEvidence
positiveDepth
Pileup
postNext
SkippableLociIterator ContigCoverageIterator
prefixTable
DeBruijnGraph
prettyPrint
LociMap
print
DelayedMessages
printFilterProgress
GenotypeFilter SomaticGenotypeFilter
printGenotypeConcordance
Concordance
printPartitioningStats
LociPartitionerArgs
printStats
Arguments
probabilityCorrectIgnoringAlignment
PileupElement
probabilityCorrectIncludingAlignment
PileupElement
progress
LoggingUtils