htsjdk.beta.codecs.reads.cram.cramV2_1

Class CRAMEncoderV2_1

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMEncoder

htsjdk.beta.codecs.reads.cram.cramV2_1.CRAMEncoderV2_1

All Implemented Interfaces:

HtsEncoder<SAMFileHeader,SAMRecord>, ReadsEncoder, java.io.Closeable, java.lang.AutoCloseable

public class CRAMEncoderV2_1
extends CRAMEncoder

CRAM v2.1 encoder.

Constructor Summary

Constructors

Constructor and Description
CRAMEncoderV2_1(Bundle outputBundle, ReadsEncoderOptions readsEncoderOptions) Create a CRAM encoder for the given output bundle.

Method Summary

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

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

close, getCRAMReferenceSource, getDisplayName, getFileFormat, getOutputBundle, getReadsEncoderOptions, setHeader, write

Methods inherited from class java.lang.Object

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

Constructor Detail

CRAMEncoderV2_1

public CRAMEncoderV2_1(Bundle outputBundle,
                       ReadsEncoderOptions readsEncoderOptions)

Create a CRAM encoder for the given output bundle. The primary resource in the bundle must have content type BundleResourceType.ALIGNED_READS (to find a decoder for a bundle, see ReadsResolver).

Parameters:

outputBundle - bundle to encode

readsEncoderOptions - options to use

Method Detail

getVersion

public HtsVersion getVersion()

Description copied from interface: HtsEncoder

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