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.

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]

### Value Members

1. #### object AlignmentRecordRDD extends Serializable

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

   InFormatter companion for building an InFormatter that streams BAM.

3. #### object FASTQInFormatter extends InFormatterCompanion[AlignmentRecord, AlignmentRecordRDD, 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 SAMInFormatter extends AnySAMInFormatterCompanion[SAMInFormatter] with Serializable

   InFormatter companion for building an InFormatter that streams SAM.

### Ungrouped