vcfstats

Type Members

1. case class Args(inputFile: File = null, outputDir: File = null, referenceFile: File = null, intervals: Option[File] = None, infoTags: List[VcfField] = Nil, genotypeTags: List[VcfField] = Nil, binSize: Int = 10000000, maxContigsInSingleJob: Int = 250, writeBinStats: Boolean = false, localThreads: Int = 1, repartition: Boolean = false, executeModulesAsJobs: Boolean = false, notWriteContigStats: Boolean = false, sparkMaster: Option[String] = None, sparkConfigValues: Map[String, String] = ..., contigSampleOverlapPlots: Boolean = false, sampleToSampleMinDepth: Option[Int] = None, skipGeneral: Boolean = false, skipGenotype: Boolean = false, skipSampleDistributions: Boolean = false, skipSampleCompare: Boolean = false) extends Product with Serializable

   

2. class ArgsParser extends AbstractOptParser[Args]

   

3. case class StatsTotal(general: Option[GeneralStats], genotype: Option[GenotypeStats], sampleDistributions: Option[SampleDistributions], sampleCompare: Option[SampleCompare], infoFields: Map[VcfField, InfoFieldCounts], genotypeFields: Map[VcfField, GenotypeFieldCounts]) extends Product with Serializable