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Type Members

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

2. class ADAMBAMOutputFormatHeaderLess[K] extends KeyIgnoringBAMOutputFormat[K] with Serializable

3. class ADAMCRAMOutputFormat[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable

4. class ADAMCRAMOutputFormatHeaderLess[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable

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

6. class ADAMSAMOutputFormatHeaderLess[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable

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

8. sealed trait AlignmentRecordRDD extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD]

9. trait AnySAMInFormatter[T <: AnySAMInFormatter[T]] extends InFormatter[AlignmentRecord, AlignmentRecordRDD, T]

10. trait AnySAMInFormatterCompanion[T <: AnySAMInFormatter[T]] extends InFormatterCompanion[AlignmentRecord, AlignmentRecordRDD, T]

11. class AnySAMOutFormatter extends OutFormatter[AlignmentRecord]

12. case class BAMInFormatter(header: SAMFileHeaderWritable, recordGroups: RecordGroupDictionary, converter: AlignmentRecordConverter) extends AnySAMInFormatter[BAMInFormatter] with Product with Serializable

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

14. 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

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

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

17. class InstrumentedADAMBAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

18. class InstrumentedADAMCRAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

19. class InstrumentedADAMCRAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

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

21. class InstrumentedADAMSAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

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

23. case class SAMInFormatter(header: SAMFileHeaderWritable, recordGroups: RecordGroupDictionary, converter: AlignmentRecordConverter) extends AnySAMInFormatter[SAMInFormatter] with Product with Serializable

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