Main
guacamole
MapBackedReferenceSequence
ReferenceBroadcast
MappedRead
reads
MappedReadSerializer
reads
Match
AlignmentState
pileup
MatchOrMisMatch
pileup
MateAlignmentProperties
reads
Micro
LociPartitionerType
MicroPartitionIndex
MicroRegionPartitioner
MicroRegionPartitioner
partitioning
MicroRegionPartitionerArgs
partitioning
MidDeletion
pileup
MinimumAlternateReadDepthFilter
genotype
MinimumLikelihoodFilter
genotype
Mismatch
AlignmentState
pileup
MultiSampleAnnotations
annotation
MultiSampleMultiAlleleEvidence
evidence
MultiSampleSingleAlleleEvidence
evidence
MultiplePileupStats
pileup_summarization
main
Main
make
MultiSampleMultiAlleleEvidence
makeCalls
SomaticJoint
makeCappedLociSets
CoverageRDD
makeHtsjdVariantContext
VCFOutput
map
loci
LociPartitioning
mapPartitions
PartitionedRegions
mappedPairedReads
ReadsRDD
mappedReads
ReadsRDD
mappedReadsRDDs
ReadSets
mateAlignmentProperties
PairedRead
maxAllelesPerSite
Parameters
CommandlineArguments
maxCallsPerSite
Parameters
CommandlineArguments
maxGenotypes
GenotypeOutputArgs
maxReadDepth
GenotypeFilterArguments
maxReadsPerPartition
CappedRegionsPartitionerArgs
maxTumorReadDepth
SomaticGenotypeFilterArguments
maximumMedianMismatches
SomaticGenotypeFilterArguments
meanBaseQuality
ReadSubsequence
AlleleEvidence
meanMappingQuality
AlleleEvidence
medianBaseQuality
AlleleEvidence
medianMappingQuality
AlleleEvidence
medianMismatchesPerRead
AlleleEvidence
mergeIndex
DeBruijnGraph
mergeOverlappingSequences
DeBruijnGraph
minAlignmentQuality
InputFilters
ReadFilterArgs
minAlternateReadDepth
GenotypeFilterArguments
minAreaVaf
AssemblyArgs
minAverageBaseQuality
Arguments
GenotypeFilterArguments
SomaticGenotypeFilterArguments
minAverageMappingQuality
GenotypeFilterArguments
SomaticGenotypeFilterArguments
minLOD
SomaticGenotypeFilterArguments
minLikelihood
Arguments
GenotypeFilterArguments
SomaticGenotypeFilterArguments
minMeanKmerQuality
AssemblyArgs
minNormalReadDepth
SomaticGenotypeFilterArguments
minOccurrence
AssemblyArgs
minReadDepth
Arguments
GenotypeFilterArguments
minTumorAlternateReadDepth
SomaticGenotypeFilterArguments
minTumorReadDepth
SomaticGenotypeFilterArguments
minVAF
Arguments
SomaticGenotypeFilterArguments
msg
RegionsNotSortedException
RepeatedContigException