htsjdk.beta.plugin.reads

Interface ReadsQuery<R extends HtsRecord>

All Known Subinterfaces:

ReadsDecoder

All Known Implementing Classes:

BAMDecoder, BAMDecoderV1_0, CRAMDecoder, CRAMDecoderV2_1, CRAMDecoderV3_0, HtsgetBAMDecoder, HtsgetBAMDecoderV1_2, SAMDecoder, SAMDecoderV1_0

public interface ReadsQuery<R extends HtsRecord>

Query methods specific to ReadsDecoders.

Method Summary

Modifier and Type	Method and Description
java.util.Optional<R>	queryMate(R record) Fetch the mate for the given read.
CloseableIterator<R>	queryUnmapped() Get an iterator of unmapped reads.

Method Detail

queryUnmapped

CloseableIterator<R> queryUnmapped()

Get an iterator of unmapped reads.

queryMate

java.util.Optional<R> queryMate(R record)

Fetch the mate for the given read.

Parameters:

record - the source record

Returns:

the source record's mate, or Optional.empty() if the source record has no mate