CalculateDepth
cli
CalculateDepthArgs
cli
CommandGroup
ADAMMain
CompareADAM
cli
CompareADAMArgs
cli
CountKmers
cli
CountKmersArgs
cli
cartesian
CalculateDepthArgs
chooseAllele
AlleleCountHelper
cli
adam
coalesce
ADAM2VcfArgs TransformArgs Vcf2ADAMArgs
commandDescription
ADAM2Vcf ADAMCommandCompanion AlleleCount Bam2ADAM BuildInformation CalculateDepth CompareADAM CountKmers Fasta2ADAM Features2ADAM FindReads FlagStat GenotypeConcordance IndexFlatGenotype ListDict MpileupCommand PileupAggregator PluginExecutor PrintADAM PrintParquet PrintTags Reads2Ref SummarizeGenotypes Transform Vcf2ADAM Vcf2FlatGenotype VcfAnnotation2ADAM VizReads
commandName
ADAM2Vcf ADAMCommandCompanion AlleleCount Bam2ADAM BuildInformation CalculateDepth CompareADAM CountKmers Fasta2ADAM Features2ADAM FindReads FlagStat GenotypeConcordance IndexFlatGenotype ListDict MpileupCommand PileupAggregator PluginExecutor PrintADAM PrintParquet PrintTags Reads2Ref SummarizeGenotypes Transform Vcf2ADAM Vcf2FlatGenotype VcfAnnotation2ADAM VizReads
commands
CommandGroup
companion
ADAM2Vcf ADAMCommand AlleleCount Bam2ADAM BuildInformation CalculateDepth CompareADAM CountKmers Fasta2ADAM Features2ADAM FindReads FlagStat GenotypeConcordance IndexFlatGenotype ListDict MpileupCommand PileupAggregator PluginExecutor PrintADAM PrintParquet PrintTags Reads2Ref SummarizeGenotypes Transform Vcf2ADAM Vcf2FlatGenotype VcfAnnotation2ADAM VizReads
comparisons
CompareADAMArgs
compressionCodec
ParquetArgs
count
PrintParquetArgs PrintTagsArgs
countAlleles
AlleleCountHelper
countQmers
CountKmersArgs
currentAnnotations
VcfAnnotation2ADAMArgs