org.bdgenomics.adam.rdd

# read

#### package read

Visibility

1. Public
2. All

### Type Members

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

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

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

   K

     The key type. Keys are not written.

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

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

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

   K

     The key type. Keys are not written.

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

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

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

   K

     The key type. Keys are not written.

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

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

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

   K

     The key type. Keys are not written.

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

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

7. #### sealed abstract class AlignmentDataset extends AvroReadGroupGenomicDataset[Alignment, Alignment, AlignmentDataset]

8. #### trait AnySAMInFormatter[T <: AnySAMInFormatter[T]] extends InFormatter[Alignment, Alignment, AlignmentDataset, T]

   A trait that writes reads using an Htsjdk SAMFileWriter.

   A trait that writes reads using an Htsjdk SAMFileWriter.

   T

     The recursive type of the class that implements this trait.

9. #### trait AnySAMInFormatterCompanion[T <: AnySAMInFormatter[T]] extends InFormatterCompanion[Alignment, Alignment, AlignmentDataset, T]

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

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

   T

     The type of the underlying InFormatter.

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

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

    An OutFormatter that automatically infers whether the piped input is SAM or BAM. Autodetecting streamed CRAM is not currently supported.

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

12. #### case class DatasetBoundAlignmentDataset extends AlignmentDataset with DatasetBoundGenomicDataset[Alignment, Alignment, AlignmentDataset] with Product with Serializable

13. #### case class DatasetBoundReadDataset extends ReadDataset with DatasetBoundGenomicDataset[Read, Read, ReadDataset] with Product with Serializable

14. #### class FASTQInFormatter extends InFormatter[Alignment, Alignment, AlignmentDataset, FASTQInFormatter]

15. #### case class IncorrectMDTagException(read: Alignment, 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.

    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.

    read

      The read whose MD tag was recomputed, with original MD tag.

    mdTag

      The recomputed MD tag.

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

    Wrapper that adds instrumentation to the BAM output format.

    Wrapper that adds instrumentation to the BAM output format.

    K

      The key type. Keys are not written.

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

    Wrapper that adds instrumentation to the SAM output format.

    Wrapper that adds instrumentation to the SAM output format.

    K

      The key type. Keys are not written.

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

    Wrapper that adds instrumentation to the CRAM output format.

    Wrapper that adds instrumentation to the CRAM output format.

    K

      The key type. Keys are not written.

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

    Wrapper that adds instrumentation to the CRAM output format.

    Wrapper that adds instrumentation to the CRAM output format.

    K

      The key type. Keys are not written.

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

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

22. #### case class ParquetUnboundAlignmentDataset extends AlignmentDataset with Product with Serializable

23. #### case class ParquetUnboundReadDataset extends ReadDataset with Product with Serializable

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

    A bin to put quality scores in.

    A bin to put quality scores in.

    low

      The lowest quality score in the bin.

    high

      The highest quality score in the bin.

    score

      The score to assign to all these bases.

25. #### case class RDDBoundAlignmentDataset extends AlignmentDataset with Product with Serializable

26. #### case class RDDBoundReadDataset extends ReadDataset with Product with Serializable

27. #### sealed abstract class ReadDataset extends AvroGenomicDataset[Read, Read, ReadDataset]

28. #### class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]

29. #### case class SAMInFormatter extends AnySAMInFormatter[SAMInFormatter] with Product with Serializable

30. #### class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

### Value Members

1. #### object AlignmentDataset extends Serializable

2. #### object BAMInFormatter extends AnySAMInFormatterCompanion[BAMInFormatter] with Serializable

   InFormatter companion for building an InFormatter that streams BAM.

3. #### object FASTQInFormatter extends InFormatterCompanion[Alignment, Alignment, AlignmentDataset, FASTQInFormatter] with Serializable

   InFormatter companion that creates an InFormatter that writes FASTQ.

4. #### object QualityScoreBin extends Serializable

   Companion object for creating quality score bins.

5. #### object ReadDataset

6. #### object SAMInFormatter extends AnySAMInFormatterCompanion[SAMInFormatter] with Serializable

   InFormatter companion for building an InFormatter that streams SAM.

### Ungrouped