RNA
Analyte
Read
reads
ReadAlignment
alignment
ReadDepthFilter
genotype
ReadFilterArgs
io
ReadSets
readsets
ReadSubsequence
pileup_summarization
ReadsRDD
rdd
ReferenceArgs
args
ReferenceBroadcast
reference
ReferenceGenome
reference
ReferenceRegion
reference
ReferenceVariant
variants
RegionsByContig
distributed
RegionsNotSortedException
iterator
Registrar
kryo
kryo
RepeatedContigException
iterator
rangeSizeStats
LociPartitioning
ranges
LociRanges
Contig
rawSortedRegions
SlidingWindow
rdd
readsets
read
ReadSubsequence
ContigSerializer
Serializer
ContigSerializer
Serializer
PileupElement
MappedReadSerializer
PairedRead
UnmappedReadSerializer
AlleleSerializer
readDepth
AlleleEvidence
readFasta
ReferenceBroadcast
readNamesByAllele
PileupStats
readPartialFasta
ReferenceBroadcast
readPosition
PileupElement
reads
guacamole
SingleSampleArgs
ReadsRDD
readsRDDs
ReadSets
readsets
guacamole
ref
AlleleAtLocus
PileupStats
refBases
Allele
refEndIdx
ReadAlignment
refSequence
ReadSubsequence
refStartIdx
ReadAlignment
reference
AlleleCount
HasReference
guacamole
referenceBase
MatchOrMisMatch
MidDeletion
Mismatch
Pileup
PileupElement
referenceBases
Deletion
Insertion
MatchOrMisMatch
MidDeletion
PileupElement
referenceDepth
Pileup
referenceElements
Pileup
referenceIsPartial
HasReference
ReferenceArgs
referenceLength
ReadSubsequence
referencePath
HasReference
ReferenceArgs
referenceReads
InsufficientNormal
referenceSequence
MultiplePileupStats
PileupStats
referenceStringIndex
PileupElement
regionStr
ReferenceRegion
registerClasses
Registrar
Registrar
registerKryo
Position
result
ParsedLoci
reverseComplement
Bases
rna
Input
rsID
CalledAllele
CalledSomaticAllele
ReferenceVariant
run
Command
PartitionLoci
PartitionReads
Caller
SparkCommand
Caller
Caller
GenotypeOutputCaller