C
Bases
CallLociArgs
args
CalledAllele
variants
CalledSomaticAllele
variants
Caller
GermlineAssemblyCaller
SomaticJoint
SomaticStandard
VAFHistogram
VariantSupport
Capped
LociPartitionerType
CappedRegionsPartitioner
partitioning
CappedRegionsPartitionerArgs
partitioning
CigarUtils
util
Clipped
pileup
Command
commands
CommandlineArguments
Parameters
Concordance
variants
ConcordanceArgs
Concordance
Contig
map
set
ContigCoverageIterator
iterator
ContigIterator
reference
ContigLengths
readsets
ContigName
reference
ContigNotFound
reference
ContigSequence
reference
ContigSerializer
map
set
ContigsIterator
iterator
Coverage
loci
CoverageRDD
rdd
children
DeBruijnGraph
chromosome
ConcordanceArgs
cigar
MappedRead
cigarElement
PileupElement
cigarElementEndLocus
PileupElement
cigarElementIndex
PileupElement
cigarElementLocus
PileupElement
cigarElementReadLength
PileupElement
cigarElementReferenceLength
PileupElement
cigarElements
MappedRead
cigarKey
AlignmentState
cluster
Arguments
commands
guacamole
compare
Interval
BasesOrdering
Allele
complement
Bases
compressReadPartitions
PartitionedRegionsArgs
computePrecisionAndRecall
Concordance
computeVariants
Caller
Caller
GenotypeOutputCaller
contains
Contig
Interval
contigAndLoci
ParsedLociRange
contigLengths
ReadSets
contigName
VariantLocus
AlleleCount
AlleleAtLocus
MultiSampleMultiAlleleEvidence
LociRange
Pileup
MappedRead
MateAlignmentProperties
ContigIterator
ContigNotFound
HasContig
Position
ArrayBackedReferenceSequence
MapBackedReferenceSequence
ReferenceRegion
CalledAllele
CalledSomaticAllele
SlidingWindow
contigOnly
ParsedLociRange
contigRegions
ContigsIterator
contigSequence
Pileup
PileupElement
contigs
LociMap
LociSet
contigsCoverages
TakeLociIterator
count
AlleleCount
LociMap
Contig
LociSet
countOfMismatches
MappedRead
coverage
CoverageRDD
currentCigarElementContainsLocus
PileupElement
currentLocus
SlidingWindow
currentRegions
SlidingWindow