cli

class CompareADAM extends BDGSparkCommand[CompareADAMArgs] with Serializable
class CompareADAMArgs extends Args4jBase with ParquetArgs with Serializable
class ComputeAlleleFrequency extends BDGSparkCommand[ComputeAlleleFrequencyArgs]
class ComputeAlleleFrequencyArgs extends Args4jBase
class Coverage extends BDGSparkCommand[CoverageArgs]
class CoverageArgs extends Args4jBase
class EstimateContamination extends BDGSparkCommand[EstimateContaminationArgs]
class EstimateContaminationArgs extends Args4jBase
class FindReads extends BDGSparkCommand[FindReadsArgs] with Serializable
class FindReadsArgs extends Args4jBase with ParquetArgs with Serializable
class GenotypeConcordance extends BDGSparkCommand[GenotypeConcordanceArgs] with Logging
class GenotypeConcordanceArgs extends Args4jBase with ParquetArgs
class LoadAlleleFrequency extends BDGSparkCommand[LoadAlleleFrequencyArgs]
class LoadAlleleFrequencyArgs extends Args4jBase
class PanelMetrics extends BDGSparkCommand[PanelMetricsArgs]
class PanelMetricsArgs extends Args4jBase
class RNAMetrics extends BDGSparkCommand[RNAMetricsArgs]
class RNAMetricsArgs extends Args4jBase
class SummarizeGenotypes extends BDGSparkCommand[SummarizeGenotypesArgs] with Logging
class SummarizeGenotypesArgs extends Args4jBase with ParquetArgs

object CompareADAM extends BDGCommandCompanion with Serializable

CompareADAM is a tool for pairwise comparison of ADAM files (or merged sets of ADAM files, see the note on the -recurse{1,2} optional parameters, below).
object ComputeAlleleFrequency extends BDGCommandCompanion
object Coverage extends BDGCommandCompanion
object EstimateContamination extends BDGCommandCompanion
object FindReads extends BDGCommandCompanion with Serializable

FindReads is an auxiliary command to CompareADAM -- whereas CompareADAM takes two ADAM files (which presumably contain the same reads, processed differently), joins them based on read-name, and computes aggregates of one or more metrics (BucketComparisons) across those joined reads -- FindReads performs the same join-and-metric-computation, but takes a second argument as well: a boolean condition on the value(s) of the metric(s) computed.
object GenotypeConcordance extends BDGCommandCompanion
object LoadAlleleFrequency extends BDGCommandCompanion
object PanelMetrics extends BDGCommandCompanion
object QuinineMain extends Logging
object RNAMetrics extends BDGCommandCompanion
object SummarizeGenotypes extends BDGCommandCompanion