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. #### 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.

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.

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

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

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.

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

    Wrapper that adds instrumentation to the BAM output format.

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

    Wrapper that adds instrumentation to the SAM output format.

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

    Wrapper that adds instrumentation to the CRAM output format.

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

    Wrapper that adds instrumentation to the CRAM output format.

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