CRAMDecoderV3_1 (htsjdk 4.3.0 API)

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMDecoder

htsjdk.beta.codecs.reads.cram.cramV3_1.CRAMDecoderV3_1

All Implemented Interfaces:: HtsDecoder<SAMFileHeader,SAMRecord>, HtsQuery<SAMRecord>, ReadsDecoder, ReadsQuery<SAMRecord>, Closeable, AutoCloseable, Iterable<SAMRecord>

public class CRAMDecoderV3_1 extends CRAMDecoder

CRAM v3.1 decoder.

Constructor Summary

Constructors

Constructor

Description

CRAMDecoderV3_1(Bundle bundle, ReadsDecoderOptions readsDecoderOptions)

Create a new CRAM v3.1 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
- CRAMDecoderV3_1
  
  public CRAMDecoderV3_1(Bundle bundle, ReadsDecoderOptions readsDecoderOptions)
  
  Create a new CRAM v3.1 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 - input Bundle to decode
  
  readsDecoderOptions - 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.