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Type Members

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

   Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

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

   Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

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

   Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

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

   Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

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

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

7. sealed abstract class AlignmentRecordRDD extends AvroRecordGroupGenomicRDD[AlignmentRecord, AlignmentRecord, AlignmentRecordRDD]

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

   A trait that writes reads using an Htsjdk SAMFileWriter.

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

   Companion object that builds an InFormatter that writes data where the metadata is contained in a SAMFileHeaderWritable.

10. case class AnySAMOutFormatter(stringency: ValidationStringency) extends OutFormatter[AlignmentRecord] with Product with Serializable

    An OutFormatter that automatically infers whether the piped input is SAM or BAM.

11. case class BAMInFormatter extends AnySAMInFormatter[BAMInFormatter] with Product with Serializable

12. case class DatasetBoundAlignmentRecordRDD extends AlignmentRecordRDD with Product with Serializable

13. class FASTQInFormatter extends InFormatter[AlignmentRecord, AlignmentRecordRDD, FASTQInFormatter] with Logging

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

    A class describing an exception where a read's MD tag was recomputed and did not match the MD tag originally attached to the read.

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

    Wrapper that adds instrumentation to the BAM output format.

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

    Wrapper that adds instrumentation to the SAM output format.

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

    Wrapper that adds instrumentation to the CRAM output format.

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

    Wrapper that adds instrumentation to the CRAM output format.

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

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

21. case class ParquetUnboundAlignmentRecordRDD extends AlignmentRecordRDD with Product with Serializable

22. case class QualityScoreBin(low: Int, high: Int, score: Int) extends Product with Serializable

    A bin to put quality scores in.

23. case class RDDBoundAlignmentRecordRDD extends AlignmentRecordRDD with Product with Serializable

24. class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]

25. case class SAMInFormatter extends AnySAMInFormatter[SAMInFormatter] with Product with Serializable

26. class SingleReadBucketSerializer extends Serializer[SingleReadBucket]