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. #### 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]

   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.

10. #### 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.

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

    T

      The type of the underlying InFormatter.

11. #### class AnySAMOutFormatter extends OutFormatter[AlignmentRecord]

    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.

12. #### 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.

    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.

13. #### 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.

14. #### 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.

15. #### 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.

16. #### 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.

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

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

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

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

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

### Value Members

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

   InFormatter companion for building an InFormatter that streams BAM.

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

   InFormatter companion for building an InFormatter that streams SAM.

3. #### object UnalignedReadRDD extends Serializable

4. #### package recalibration

### Ungrouped