SampleId
readsets
SampleName
readsets
SampleRegion
reads
Sequence
DeBruijnGraph
Serializer
map set
SingleContigRegionIterator
distributed
SingleSampleAnnotations
annotation
SingleSampleArgs
args
SingleSampleSingleAlleleEvidence
evidence
SkippableLociIterator
iterator
SkippableLocusKeyedIterator
iterator
SlidingWindow
windowing
SomaticAlternateReadDepthFilter
somatic
SomaticAverageBaseQualityFilter
somatic
SomaticAverageMappingQualityFilter
somatic
SomaticGenotypeFilter
somatic
SomaticGenotypeFilterArguments
SomaticGenotypeFilter
SomaticGenotypePolicy
Parameters
SomaticJoint
commands
SomaticLogOddsFilter
somatic
SomaticMedianMismatchFilter
somatic
SomaticMinimumLikelihoodFilter
somatic
SomaticReadDepthFilter
somatic
SomaticStandard
commands
SomaticVAFFilter
somatic
SparkCommand
commands
SplitIterator
windowing
StrandBias
annotation
SubKmer
DeBruijnGraph
sampleEvidences
MultiSampleSingleAlleleEvidence
sampleId
VariantLocus HasSampleId MappedRead PairedRead UnmappedRead
sampleName
AlleleCount Input Pileup SingleSampleArgs Input CalledAllele CalledSomaticAllele ReferenceVariant
sampleNames
ReadSets Arguments Base SingleSampleArgs TumorNormalReadsArgs
samplePercent
Arguments
save
LociPartitioning PartitionedRegions
say
DelayedMessages
sc
ReadSets CoverageRDD PartitionedRegions
scoreAlignmentPaths
AffineGapPenaltyAlignment
secondAlt
PileupStats
seenContigs
ContigsIterator
sequence
ReadSubsequence MappedRead PairedRead Read UnmappedRead
sequenceDictionary
ReadSets
sequenceIsAllStandardBases
ReadSubsequence
sequencedBases
Deletion Insertion MatchOrMisMatch MidDeletion PileupElement
set
loci
setCurrentLocus
SlidingWindow
setDefaultConf
SparkCommand
shortName
ReadsRDD
shortcutAssembly
AssemblyArgs
singleAlleleEvidences
MultiSampleMultiAlleleEvidence
singleSampleStats
MultiplePileupStats
sinks
DeBruijnGraph
skipTo
SkippableLociIterator
slice
MappedRead ContigSequence ArrayBackedReferenceSequence MapBackedReferenceSequence
somatic
filters
somaticGenotypePolicy
Parameters CommandlineArguments
somaticLogOdds
CalledSomaticAllele
somaticMaxGermlineErrorRatePercent
Parameters CommandlineArguments
somaticNegativeLog10VariantPrior
Parameters CommandlineArguments
somaticNegativeLog10VariantPriorRna
Parameters CommandlineArguments
somaticNegativeLog10VariantPriorWithRnaEvidence
Parameters CommandlineArguments
somaticVafFloor
Parameters CommandlineArguments
source
ReferenceBroadcast ReferenceGenome
sources
DeBruijnGraph
split
SplitIterator
splitPartitionByContigAndMap
WindowFlatMapUtils
start
AlleleAtLocus MultiSampleMultiAlleleEvidence LociRange MappedRead MateAlignmentProperties Interval Position CalledAllele CalledSomaticAllele
startLocus
ReadSubsequence
startReadPosition
ReadSubsequence
starts
Coverage
stats
breeze
strandBias
SingleSampleAnnotations
stringPieces
Contig LociMap LociPartitioning Contig LociSet TruncatedToString
stringToBases
Bases
strings
guacamole
subsequences
PileupStats
suffixTable
DeBruijnGraph