org.bdgenomics.adam.rdd

read

package read

Visibility
  1. Public
  2. All

Type Members

  1. class ADAMAlignmentRecordContext extends Serializable with Logging

  2. class ADAMAlignmentRecordRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[AlignmentRecord]

  3. class ADAMBAMOutputFormat[K] extends KeyIgnoringBAMOutputFormat[K] with Serializable

  4. class ADAMSAMOutputFormat[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable

  5. case class DuplicateMetrics(total: Long, bothMapped: Long, onlyReadMapped: Long, crossChromosome: Long) extends Product with Serializable

  6. case class FlagStatMetrics(total: Long, duplicatesPrimary: DuplicateMetrics, duplicatesSecondary: DuplicateMetrics, mapped: Long, pairedInSequencing: Long, read1: Long, read2: Long, properlyPaired: Long, withSelfAndMateMapped: Long, singleton: Long, withMateMappedToDiffChromosome: Long, withMateMappedToDiffChromosomeMapQ5: Long, failedQuality: Boolean) extends Product with Serializable

Value Members

  1. object ADAMAlignmentRecordContext extends Serializable

  2. object ADAMBAMOutputFormat extends Serializable

  3. object ADAMSAMOutputFormat extends Serializable

  4. object DuplicateMetrics extends Serializable

  5. object FlagStat

  6. object FlagStatMetrics extends Serializable

  7. package comparisons

  8. package realignment

  9. package recalibration

Ungrouped