htsjdk.beta.codecs.reads.cram.cramV3_0

Class CRAMDecoderV3_0

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMDecoder

htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMDecoderV3_0

All Implemented Interfaces:

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

public class CRAMDecoderV3_0
extends CRAMDecoder

CRAM v3.0 decoder.

Constructor Summary

Constructors

Constructor and Description
CRAMDecoderV3_0(Bundle bundle, ReadsDecoderOptions readsDecoderOptions) Create a new CRAM V3.0 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

CRAMDecoderV3_0

public CRAMDecoderV3_0(Bundle bundle,
                       ReadsDecoderOptions readsDecoderOptions)

Create a new CRAM V3.0 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 - input Bundle to decode

readsDecoderOptions - 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.