org.seqdoop.hadoop_bam

Class VariantContextWritable

java.lang.Object

org.seqdoop.hadoop_bam.VariantContextWritable

All Implemented Interfaces:

org.apache.hadoop.io.Writable

public class VariantContextWritable
extends Object
implements org.apache.hadoop.io.Writable

VariantContexts read here have LazyGenotypesContexts, which need to have a header set before the genotype data in the VariantContexts can be decoded. See the LazyGenotypesContext class.

Constructor Summary

Constructors

Constructor and Description
VariantContextWritable()

Method Summary

Modifier and Type	Method and Description
htsjdk.variant.variantcontext.VariantContext	get()
void	readFields(DataInput in)
void	set(htsjdk.variant.variantcontext.VariantContext vc)
void	set(htsjdk.variant.variantcontext.VariantContext vc, htsjdk.variant.vcf.VCFHeader header)
void	write(DataOutput out)

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantContextWritable

public VariantContextWritable()

Method Detail

get

public htsjdk.variant.variantcontext.VariantContext get()

set

public void set(htsjdk.variant.variantcontext.VariantContext vc)

set

public void set(htsjdk.variant.variantcontext.VariantContext vc,
                htsjdk.variant.vcf.VCFHeader header)

write

public void write(DataOutput out)
           throws IOException

Specified by:

write in interface org.apache.hadoop.io.Writable

Throws:

IOException

readFields

public void readFields(DataInput in)
                throws IOException

Specified by:

readFields in interface org.apache.hadoop.io.Writable

Throws:

IOException