htsjdk.beta.codecs.reads.cram.cramV2_1

Class CRAMDecoderV2_1

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMDecoder

htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMDecoderV2_1

All Implemented Interfaces:

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

public class CRAMDecoderV2_1
extends CRAMDecoder

CRAM v2.1decoder.

Constructor Summary

Constructors

Constructor and Description
CRAMDecoderV2_1(Bundle bundle, ReadsDecoderOptions readsDecoderOptions) Create a new V2.1 CRAM decoder.

Method Summary

Modifier and Type	Method and Description
HtsVersion	getVersion() Get the version of the file format supported by this decoder.

Methods inherited from class htsjdk.beta.codecs.reads.cram.CRAMDecoder

close, getCRAMReferenceSource, getDisplayName, getFileFormat, getHeader, getInputBundle, getReadsDecoderOptions, hasIndex, isQueryable, iterator, query, queryMate, queryStart, queryUnmapped

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery

query, query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

CRAMDecoderV2_1

public CRAMDecoderV2_1(Bundle bundle,
                       ReadsDecoderOptions readsDecoderOptions)

Create a new V2.1 CRAM decoder. The primary resource in the input bundle must have content type BundleResourceType.ALIGNED_READS (to find a decoder for a bundle, see ReadsResolver).

Parameters:

bundle - the input Bundle to decode

readsDecoderOptions - the ReadsDecoderOptions to use

Method Detail

getVersion

public HtsVersion getVersion()

Description copied from interface: HtsDecoder

Get the version of the file format supported by this decoder.