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 ADAMBAMOutputFormatHeaderLess[K] extends KeyIgnoringBAMOutputFormat[K] with Serializable

3. #### class ADAMSAMOutputFormat[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable

4. #### class ADAMSAMOutputFormatHeaderLess[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable

5. #### case class AlignedReadRDD(rdd: RDD[AlignmentRecord], sequences: SequenceDictionary, recordGroups: RecordGroupDictionary) extends AlignmentRecordRDD with Product with Serializable

6. #### abstract class AlignmentRecordRDD extends GenomicRDD[AlignmentRecord]

7. #### class AlignmentRecordRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[AlignmentRecord]

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

9. #### 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

10. #### case class IncorrectMDTagException(read: AlignmentRecord, mdTag: String) extends Exception with Product with Serializable

11. #### class InstrumentedADAMBAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

12. #### class InstrumentedADAMBAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

13. #### class InstrumentedADAMSAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

14. #### class InstrumentedADAMSAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

15. #### case class MDTagging(reads: RDD[AlignmentRecord], referenceFile: ReferenceFile, partitionSize: Long = 1000000, overwriteExistingTags: Boolean = false, validationStringency: ValidationStringency = ...) extends Logging with Product with Serializable

16. #### case class UnalignedReadRDD(rdd: RDD[AlignmentRecord], recordGroups: RecordGroupDictionary) extends AlignmentRecordRDD with Unaligned with Product with Serializable

### 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. #### object MDTagging extends Serializable

7. #### object UnalignedReadRDD extends Serializable

8. #### package realignment

9. #### package recalibration

### Ungrouped