Likelihood
likelihood
LociIterator
set
LociMap
map
LociPartitioner
partitioning
LociPartitionerArgs
partitioning
LociPartitionerType
partitioning
LociPartitionerType
LociPartitioning
partitioning
LociRange
parsing
LociRanges
parsing
LociSet
set
Locus
reference
LoggingUtils
logging
lastProgressTime
LoggingUtils
length
ReadSets
ContigSequence
Interval
ArrayBackedReferenceSequence
MapBackedReferenceSequence
CalledAllele
CalledSomaticAllele
likelihood
guacamole
AlleleEvidence
likelihoodOfGenotype
Likelihood
likelihoodsOfAllPossibleGenotypesFromPileup
Likelihood
load
PartitionedRegions
loadGenotypes
Concordance
localOutputPath
Arguments
loci
guacamole
InputFilters
lociFile
CallLociArgs
lociFileOpt
CallLociArgs
lociMapToLociPartitioning
LociPartitioning
lociPartitionerName
LociPartitionerArgs
lociPartitioningPathOpt
LociPartitionerArgs
PartitionedRegionsArgs
lociPartitioningToLociMap
LociPartitioning
lociSetMinusOne
SomaticJoint
lociSetsRDD
LociPartitioning
PartitionedRegions
lociStr
CallLociArgs
lociStrOpt
CallLociArgs
locus
VariantLocus
AlleleCount
SkippableLociIterator
Pileup
PileupElement
HasLocus
Position
locusFn
SkippableLociIterator
SkippableLocusKeyedIterator
LociIterator
logLikelihoodPileup
PileupStats
logLikelihoods
NormalDNASingleSampleSingleAlleleEvidence
TumorDNASingleSampleSingleAlleleEvidence
TumorRNASingleSampleSingleAlleleEvidence
logging
guacamole