CalculateDepth
cli
CalculateDepthArgs
cli
CommandGroup
cli
CountContigKmers
cli
CountContigKmersArgs
cli
CountReadKmers
cli
CountReadKmersArgs
cli
cache
TransformArgs
chooseAllele
AlleleCountHelper
cli
adam
coalesce
ADAM2FastaArgs ADAM2VcfArgs TransformArgs Vcf2ADAMArgs
collapse
Reads2CoverageArgs
commandDescription
ADAM2Fasta ADAM2Fastq ADAM2Vcf AlleleCount CalculateDepth CountContigKmers CountReadKmers Fasta2ADAM FlagStat Flatten Fragments2Reads ListDict MergeShards PrintADAM Reads2Coverage Reads2Fragments Transform TransformFeatures Vcf2ADAM VcfAnnotation2ADAM View WigFix2Bed
commandName
ADAM2Fasta ADAM2Fastq ADAM2Vcf AlleleCount CalculateDepth CountContigKmers CountReadKmers Fasta2ADAM FlagStat Flatten Fragments2Reads ListDict MergeShards PrintADAM Reads2Coverage Reads2Fragments Transform TransformFeatures Vcf2ADAM VcfAnnotation2ADAM View WigFix2Bed
commands
CommandGroup
commit
About
companion
ADAM2Fasta ADAM2Fastq ADAM2Vcf AlleleCount CalculateDepth CountContigKmers CountReadKmers Fasta2ADAM FlagStat Flatten Fragments2Reads ListDict MergeShards PrintADAM Reads2Coverage Reads2Fragments Transform TransformFeatures Vcf2ADAM VcfAnnotation2ADAM View WigFix2Bed
concatFilename
TransformArgs
configure
ADAMModule
countAlleles
AlleleCountHelper
cramEof
MergeShardsArgs
currentAnnotations
VcfAnnotation2ADAMArgs