htsjdk.beta.codecs.variants.vcf.vcfv4_2

Class VCFDecoderV4_2

java.lang.Object

htsjdk.beta.codecs.variants.vcf.VCFDecoder

htsjdk.beta.codecs.variants.vcf.vcfv4_2.VCFDecoderV4_2

All Implemented Interfaces:

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

public class VCFDecoderV4_2
extends VCFDecoder

VCF V4.2 decoder.

Constructor Summary

Constructors

Constructor and Description
VCFDecoderV4_2(Bundle inputBundle, VariantsDecoderOptions variantsDecoderOptions) Create a new VCF V4.2 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

VCFDecoderV4_2

public VCFDecoderV4_2(Bundle inputBundle,
                      VariantsDecoderOptions variantsDecoderOptions)

Create a new VCF V4.2 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.