A
Bases
ALT
Bases
AffineGapPenaltyAlignment
alignment
AlignmentState
alignment
AlignmentState
All
parsing
AllRange
parsing
Allele
variants
AlleleAtLocus
jointcaller
AlleleCount
Caller
AlleleEvidence
variants
AlleleMixture
PileupStats
AlleleSerializer
variants
Analyte
Input
Annotation
MultiSampleAnnotations
SingleSampleAnnotations
Args
commands
Arguments
GermlineAssemblyCaller
SomaticJoint
SomaticStandard
VAFHistogram
VariantSupport
InputCollection
args
ArrayBackedReferenceSequence
ReferenceBroadcast
AssemblyArgs
assembly
AssemblyUtils
assembly
AverageBaseQualityFilter
genotype
AverageMappingQualityFilter
genotype
addInfoToVCF
MultiSampleAnnotations
Annotation
SingleSampleAnnotations
Annotation
StrandBias
addVCFHeaders
InsufficientNormal
MultiSampleAnnotations
SingleSampleAnnotations
StrandBias
TooManyCallsAtSite
advanceMultipleWindows
SlidingWindow
advanceToLocus
PileupElement
advanceToNextCigarElement
PileupElement
align
AffineGapPenaltyAlignment
alignment
guacamole
PileupElement
alignmentLikelihood
MappedRead
alignmentQuality
MappedRead
alignmentScore
ReadAlignment
alignments
ReadAlignment
all
ParsedLoci
LociSet
allEvidences
MultiSampleSingleAlleleEvidence
allMappedReads
ReadSets
allStandardBases
Bases
allele
MultiSampleSingleAlleleEvidence
NormalDNASingleSampleSingleAlleleEvidence
SingleSampleSingleAlleleEvidence
TumorDNASingleSampleSingleAlleleEvidence
TumorRNASingleSampleSingleAlleleEvidence
PileupElement
CalledAllele
CalledSomaticAllele
ReferenceVariant
alleleForwardDepth
AlleleEvidence
alleleMixture
Genotype
alleleReadDepth
AlleleEvidence
alleleReadDepthAndPositiveDepth
Pileup
alleleSerializer
HasAlleleSerializer
alleleToSubsequences
PileupStats
alleles
Genotype
allelesToMixture
NormalDNASingleSampleSingleAlleleEvidence
allelicDepths
NormalDNASingleSampleSingleAlleleEvidence
TumorDNASingleSampleSingleAlleleEvidence
TumorRNASingleSampleSingleAlleleEvidence
PileupStats
alt
AlleleAtLocus
altBases
Allele
alternate
AlleleCount
analyte
Input
analytes
Arguments
annotate
MultiSampleSingleAlleleEvidence
annotation
jointcaller
annotations
MultiSampleSingleAlleleEvidence
NormalDNASingleSampleSingleAlleleEvidence
SingleSampleSingleAlleleEvidence
TumorDNASingleSampleSingleAlleleEvidence
TumorRNASingleSampleSingleAlleleEvidence
annotationsFailingFilters
MultiSampleAnnotations
SingleSampleAnnotations
anyAlleleMinSupportingPercent
Parameters
CommandlineArguments
anyAlleleMinSupportingReads
Parameters
CommandlineArguments
apply
DeBruijnGraph
VariantLocus
FishersExactTest
AverageBaseQualityFilter
AverageMappingQualityFilter
GenotypeFilter
MinimumAlternateReadDepthFilter
MinimumLikelihoodFilter
ReadDepthFilter
SomaticAlternateReadDepthFilter
SomaticAverageBaseQualityFilter
SomaticAverageMappingQualityFilter
SomaticGenotypeFilter
SomaticLogOddsFilter
SomaticMedianMismatchFilter
SomaticMinimumLikelihoodFilter
SomaticReadDepthFilter
SomaticVAFFilter
InputCollection
Parameters
InsufficientNormal
MultiSampleAnnotations
SingleSampleAnnotations
StrandBias
TooManyCallsAtSite
MultiSampleSingleAlleleEvidence
NormalDNASingleSampleSingleAlleleEvidence
TumorDNASingleSampleSingleAlleleEvidence
TumorRNASingleSampleSingleAlleleEvidence
PileupStats
Contig
LociMap
LociRange
ParsedLoci
ParsedLociRange
ParsedLociRanges
LociPartitioning
LociSet
DelayedMessages
Deletion
Pileup
PileupElement
MateAlignmentProperties
Read
ReadSets
Input
ContigsIterator
PartitionedRegions
ContigIterator
ContigSequence
Interval
Position
ReferenceBroadcast
ArrayBackedReferenceSequence
MapBackedReferenceSequence
ReferenceRegion
TruncatedToString
Allele
AlleleEvidence
args
loci
readsets
asLog
FishersExactTest
asLog10
FishersExactTest
asMap
Contig
asMappedRead
MappedRead
PairedRead
Read
UnmappedRead
asStringPairs
Parameters
assembly
guacamole
assemblyWindowRange
AssemblyArgs
assertAllStandardBases
Bases
assertStandardBase
Bases
atGreaterLocus
Pileup
availableContigs
ContigNotFound