org.bdgenomics.adam.rdd

read

package read

Visibility
  1. Public
  2. All

Type Members

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

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

  3. class AlignmentRecordRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[AlignmentRecord]

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

  5. 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

  6. class InstrumentedADAMBAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

  7. class InstrumentedADAMSAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

Value Members

  1. object ADAMBAMOutputFormat extends Serializable

  2. object ADAMSAMOutputFormat extends Serializable

  3. object DuplicateMetrics extends Serializable

  4. object FlagStat

  5. object FlagStatMetrics extends Serializable

  6. package realignment

  7. package recalibration

Ungrouped