htsjdk.beta.codecs.reads.cram.cramV3_0

Class CRAMEncoderV3_0

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMEncoder

htsjdk.beta.codecs.reads.cram.cramV3_0.CRAMEncoderV3_0

All Implemented Interfaces:

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

public class CRAMEncoderV3_0
extends CRAMEncoder

CRAM v3.0 encoder.

Constructor Summary

Constructors

Constructor and Description
CRAMEncoderV3_0(Bundle outputBundle, ReadsEncoderOptions readsEncoderOptions) Create a new CRAM CRAM v3.0 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

CRAMEncoderV3_0

public CRAMEncoderV3_0(Bundle outputBundle,
                       ReadsEncoderOptions readsEncoderOptions)

Create a new CRAM CRAM v3.0 encoder for the given output bundle. The primary resource in the bundle must have content type BundleResourceType.ALIGNED_READS (to find an encoder for a bundle, see ReadsResolver).

Parameters:

outputBundle - output Bundle to encode

readsEncoderOptions - ReadsEncoderOptions to use

Method Detail

getVersion

public HtsVersion getVersion()

Description copied from interface: HtsEncoder

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