CRAMEncoderV3_1 (htsjdk 4.3.0 API)

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMEncoder

htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMEncoderV3_1

All Implemented Interfaces:: HtsEncoder<SAMFileHeader,SAMRecord>, ReadsEncoder, Closeable, AutoCloseable

public class CRAMEncoderV3_1 extends CRAMEncoder

CRAM v3.1 encoder.

Constructor Summary

Constructors

Constructor

Description

CRAMEncoderV3_1(Bundle outputBundle, ReadsEncoderOptions readsEncoderOptions)

Create a new CRAM v3.1 encoder for the given output bundle.
Method Summary

Modifier and Type

Method

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 Details
- CRAMEncoderV3_1
  
  public CRAMEncoderV3_1(Bundle outputBundle, ReadsEncoderOptions readsEncoderOptions)
  
  Create a new CRAM v3.1 encoder for the given output bundle. The primary resource in the bundle must have content type BundleResourceType.CT_ALIGNED_READS (to find an encoder for a bundle, see ReadsResolver).
  
  Parameters:
  
  outputBundle - output Bundle to encode
  
  readsEncoderOptions - ReadsEncoderOptions to use
Method Details
- getVersion
  
  public HtsVersion getVersion()
  
  Description copied from interface: HtsEncoder
  
  Get the version of the file format supported by this encoder.