htsjdk.beta.plugin.reads

Interface ReadsDecoder

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable, HtsDecoder<SAMFileHeader,SAMRecord>, HtsQuery<SAMRecord>, java.lang.Iterable<SAMRecord>, ReadsQuery<SAMRecord>

All Known Implementing Classes:

BAMDecoder, BAMDecoderV1_0, CRAMDecoder, CRAMDecoderV2_1, CRAMDecoderV3_0, 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 and Description
java.util.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 Detail

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

java.util.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