Input
jointcaller
io
InputCollection
jointcaller
InputFilters
io
Insertion
AlignmentState
pileup
InsufficientNormal
annotation
IntHist
PartitionedRegions
Interval
reference
InvalidCigarElementException
pileup
id
AlleleAtLocus
Input
includeDuplicates
ReadFilterArgs
includeFailedQualityChecks
ReadFilterArgs
includeFiltered
Arguments
includeSingleEnd
ReadFilterArgs
index
Input
indexWithinCigarElement
PileupElement
inferredInsertSize
MateAlignmentProperties
input
ReadsRDD
inputs
MultiSampleSingleAlleleEvidence
MultiplePileupStats
ReadSets
Base
insufficientNormal
MultiSampleAnnotations
intersect
SkippableLociIterator
Contig
LociSet
intersects
Contig
LociSet
intervals
ContigCoverageIterator
intraContigPartialOrdering
ReferenceRegion
inverse
Contig
LociMap
io
readsets
isActiveRegion
AssemblyUtils
isCall
MultiSampleSingleAlleleEvidence
isClipped
PileupElement
CigarUtils
isDeletion
PileupElement
isDuplicate
MappedRead
PairedRead
Read
UnmappedRead
isEmpty
Contig
LociSet
isFiltered
InsufficientNormal
Annotation
Annotation
StrandBias
TooManyCallsAtSite
isFinalCigarBase
PileupElement
isFirstInPair
PairedRead
isGapAlignment
AlignmentState
isGermlineCall
MultiSampleSingleAlleleEvidence
isInsertion
PileupElement
isMapped
MappedRead
PairedRead
Read
UnmappedRead
isMatch
PileupElement
isMateMapped
PairedRead
isMidDeletion
PileupElement
isMismatch
PileupElement
isPaired
MappedRead
PairedRead
Read
UnmappedRead
InputFilters
isPositiveStrand
MappedRead
MateAlignmentProperties
isSomaticCall
MultiSampleSingleAlleleEvidence
isStandardBase
Bases
isVariant
Allele
items
InputCollection
iterator
loci
Contig
readsets
Interval