CRAMDecoderV2_1 (htsjdk 4.3.0 API)

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>, Closeable, AutoCloseable, Iterable<SAMRecord>

public class CRAMDecoderV2_1 extends CRAMDecoder

CRAM v2.1decoder.

Constructor Summary

Constructors

Constructor

Description

CRAMDecoderV2_1(Bundle bundle, ReadsDecoderOptions readsDecoderOptions)

Create a new V2.1 CRAM decoder.
Method Summary

Modifier and Type

Method

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 Details
- 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.CT_ALIGNED_READS (to find a decoder for a bundle, see ReadsResolver).
  
  Parameters:
  
  bundle - the input Bundle to decode
  
  readsDecoderOptions - the ReadsDecoderOptions to use
Method Details
- getVersion
  
  public HtsVersion getVersion()
  
  Description copied from interface: HtsDecoder
  
  Get the version of the file format supported by this decoder.