htsjdk.beta.codecs.variants.vcf.vcfv3_3

Class VCFDecoderV3_3

java.lang.Object

htsjdk.beta.codecs.variants.vcf.VCFDecoder

htsjdk.beta.codecs.variants.vcf.vcfv3_3.VCFDecoderV3_3

All Implemented Interfaces:

HtsDecoder<VCFHeader,VariantContext>, HtsQuery<VariantContext>, VariantsDecoder, java.io.Closeable, java.lang.AutoCloseable, java.lang.Iterable<VariantContext>

public class VCFDecoderV3_3
extends VCFDecoder

VCF V3.3 decoder.

Constructor Summary

Constructors

Constructor and Description
VCFDecoderV3_3(Bundle inputBundle, VariantsDecoderOptions variantsDecoderOptions) Create a new VCF V3.3 decoder.

Method Summary

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

Methods inherited from class htsjdk.beta.codecs.variants.vcf.VCFDecoder

close, getDisplayName, getFileFormat, getHeader, getInputBundle, getReadsDecoderOptions, hasIndex, isQueryable, iterator, query, query, queryStart

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, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

VCFDecoderV3_3

public VCFDecoderV3_3(Bundle inputBundle,
                      VariantsDecoderOptions variantsDecoderOptions)

Create a new VCF V3.3 decoder.

Parameters:

inputBundle - the input Bundle to decode

variantsDecoderOptions - the VariantsDecoderOptions for this decoder

Method Detail

getVersion

public HtsVersion getVersion()

Description copied from interface: HtsDecoder

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