ADAM2Vcf
cli
ADAM2VcfArgs
cli
ADAMCommand
cli
ADAMCommandCompanion
cli
ADAMMain
cli
ADAMSparkCommand
cli
AlleleCount
cli
AlleleCountArgs
cli
AlleleCountHelper
cli
Args4j
cli
Args4jBase
cli
accessControl
PluginExecutorArgs
adam
bdgenomics
adamFile
ADAM2VcfArgs AlleleCountArgs SummarizeGenotypesArgs
adamInputPath
CalculateDepthArgs
aggregate
Reads2RefArgs
apply
ADAM2Vcf ADAMCommandCompanion AlleleCount Args4j Bam2ADAM BuildInformation CalculateDepth CompareADAM CountKmers Fasta2ADAM Features2ADAM FindReads FlagStat GenotypeConcordance IndexFlatGenotype ListDict MpileupCommand PileupAggregator PluginExecutor PrintADAM PrintParquet PrintTags Reads2Ref SummarizeGenotypes Transform Vcf2ADAM Vcf2FlatGenotype VcfAnnotation2ADAM
args
ADAM2Vcf ADAMSparkCommand AlleleCount CalculateDepth CompareADAM CountKmers Fasta2ADAM Features2ADAM FindReads FlagStat GenotypeConcordance IndexFlatGenotype ListDict MpileupCommand PileupAggregator PluginExecutor PrintADAM PrintTags Reads2Ref SummarizeGenotypes Transform Vcf2ADAM VcfAnnotation2ADAM