ReadsDecoder (htsjdk 4.3.0 API)

All Superinterfaces:: AutoCloseable, Closeable, HtsDecoder<SAMFileHeader,SAMRecord>, HtsQuery<SAMRecord>, Iterable<SAMRecord>, ReadsQuery<SAMRecord>

All Known Implementing Classes:: BAMDecoder, BAMDecoderV1_0, CRAMDecoder, CRAMDecoderV2_1, CRAMDecoderV3_0, CRAMDecoderV3_1, HtsgetBAMDecoder, HtsgetBAMDecoderV1_2, SAMDecoder, SAMDecoderV1_0

public interface ReadsDecoder extends HtsDecoder<SAMFileHeader,SAMRecord>, ReadsQuery<SAMRecord>

Base class for all HtsContentType.ALIGNED_READS decoders. Defines the type parameters instantiated for reads decoders.

Method Summary

Modifier and Type

Method

Description

Optional<SAMRecord>

queryMate(SAMRecord rec)

Fetch the mate for the given read.

CloseableIterator<SAMRecord>

queryUnmapped()

Get an iterator of unmapped reads.

Methods inherited from interface htsjdk.beta.plugin.HtsDecoder
close, getDisplayName, getFileFormat, getHeader, getVersion

Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery
hasIndex, isQueryable, iterator, query, query, query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping, queryStart

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Method Details
- queryUnmapped
  
  CloseableIterator<SAMRecord> queryUnmapped()
  
  Get an iterator of unmapped reads. Requires an index resource to be included in the input Bundle.
  
  Specified by:
  
  queryUnmapped in interface ReadsQuery<SAMRecord>
- queryMate
  
  Optional<SAMRecord> queryMate(SAMRecord rec)
  
  Fetch the mate for the given read. Requires an index resource to be included in the input Bundle.
  
  Specified by:
  
  queryMate in interface ReadsQuery<SAMRecord>
  
  Parameters:
  
  rec - the source record
  
  Returns:
  
  the source record's mate, or Optional.empty() if the source record has no mate