Packages

package common

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Type Members

  1. case class GenotypeFields(sampleId: Option[String], phased: Option[Boolean], calls: Option[Seq[Int]], depth: Option[Int], filters: Option[Seq[String]], genotypeLikelihoods: Option[Seq[Double]], phredLikelihoods: Option[Seq[Int]], posteriorProbabilities: Option[Seq[Double]], conditionalQuality: Option[Int], haplotypeQualities: Option[Seq[Int]], expectedAlleleCounts: Option[Seq[Int]], mappingQuality: Option[Int], alleleDepths: Option[Seq[Int]], otherFields: Map[String, String]) extends Product with Serializable
  2. trait GlowLogging extends LazyLogging
  3. trait HasStringency extends GlowLogging
  4. trait Named extends AnyRef
  5. case class SimpleInterval(contig: String, start: Int, end: Int) extends Locatable with Serializable with Product

    Minimal immutable class representing a 1-based closed ended genomic interval Simplified version of org.broadinstitute.hellbender.utils.SimpleInterval

  6. case class VCFRow(contigName: String, start: Long, end: Long, names: Seq[String], referenceAllele: String, alternateAlleles: Seq[String], qual: Option[Double], filters: Seq[String], attributes: Map[String, String], genotypes: Seq[GenotypeFields], splitFromMultiAllelic: Boolean = false) extends Product with Serializable

Value Members

  1. object BgenOptions
  2. object CommonOptions
  3. object FeatureSchemas
  4. object GenotypeFields extends Serializable
  5. object HailUtils
  6. object PlinkOptions
  7. object VCFOptions
  8. object VCFRow extends Serializable
  9. object VariantSchemas
  10. object WithUtils

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