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