htsjdk.variant.vcf

Class VCFRecordCodec

java.lang.Object

htsjdk.variant.vcf.VCFRecordCodec

All Implemented Interfaces:

SortingCollection.Codec<VariantContext>, java.lang.Cloneable

public class VCFRecordCodec
extends java.lang.Object
implements SortingCollection.Codec<VariantContext>

Writes VariantContext instances to an OutputStream without headers or metadata. For use with SortingCollection ONLY.

Constructor Summary

Constructors

Constructor and Description
VCFRecordCodec(VCFHeader header)

Method Summary

Methods

Modifier and Type	Method and Description
VCFRecordCodec	clone() Must return a cloned copy of the codec that can be used independently of the original instance.
VariantContext	decode() Read the next record from the input stream and convert into a java object.
void	encode(VariantContext context) Write object to output stream
void	setInputStream(java.io.InputStream stream) Where to read encoded input from
void	setOutputStream(java.io.OutputStream stream) Where to write encoded output

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

VCFRecordCodec

public VCFRecordCodec(VCFHeader header)

Method Detail

setOutputStream

public void setOutputStream(java.io.OutputStream stream)

Description copied from interface: SortingCollection.Codec

Where to write encoded output

Specified by:

setOutputStream in interface SortingCollection.Codec<VariantContext>

setInputStream

public void setInputStream(java.io.InputStream stream)

Description copied from interface: SortingCollection.Codec

Where to read encoded input from

Specified by:

setInputStream in interface SortingCollection.Codec<VariantContext>

encode

public void encode(VariantContext context)

Description copied from interface: SortingCollection.Codec

Write object to output stream

Specified by:

encode in interface SortingCollection.Codec<VariantContext>

Parameters:

context - what to write

decode

public VariantContext decode()

Description copied from interface: SortingCollection.Codec

Read the next record from the input stream and convert into a java object.

Specified by:

decode in interface SortingCollection.Codec<VariantContext>

Returns:

null if no more records. Should throw exception if EOF is encountered in the middle of a record.

clone

public VCFRecordCodec clone()

Description copied from interface: SortingCollection.Codec

Must return a cloned copy of the codec that can be used independently of the original instance. This is required so that multiple codecs can exist simultaneously that each is reading a separate file.

Specified by:

clone in interface SortingCollection.Codec<VariantContext>

Overrides:

clone in class java.lang.Object