picard.vcf

Class PairedVariantSubContextIterator

java.lang.Object

picard.vcf.PairedVariantSubContextIterator

All Implemented Interfaces:

java.util.Iterator<PairedVariantSubContextIterator.VcfTuple>

public class PairedVariantSubContextIterator
extends java.lang.Object
implements java.util.Iterator<PairedVariantSubContextIterator.VcfTuple>

An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem. A tuple will be returned with variant contexts for both contexts if present. Otherwise, the missing context at that site will be empty. The contexts will be returned in coordinate order.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PairedVariantSubContextIterator.VcfTuple Little class to hold a pair of VariantContexts that are in sync with one another.

Constructor Summary

Constructors

Constructor and Description
PairedVariantSubContextIterator(java.util.Iterator<htsjdk.variant.variantcontext.VariantContext> leftIterator, java.lang.String leftSample, java.util.Iterator<htsjdk.variant.variantcontext.VariantContext> rightIterator, java.lang.String rightSample, htsjdk.samtools.SAMSequenceDictionary dict)

Method Summary

Modifier and Type	Method and Description
boolean	hasNext()
PairedVariantSubContextIterator.VcfTuple	next()
void	remove()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

PairedVariantSubContextIterator

public PairedVariantSubContextIterator(java.util.Iterator<htsjdk.variant.variantcontext.VariantContext> leftIterator,
                                       java.lang.String leftSample,
                                       java.util.Iterator<htsjdk.variant.variantcontext.VariantContext> rightIterator,
                                       java.lang.String rightSample,
                                       htsjdk.samtools.SAMSequenceDictionary dict)

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<PairedVariantSubContextIterator.VcfTuple>

next

public PairedVariantSubContextIterator.VcfTuple next()

Specified by:

next in interface java.util.Iterator<PairedVariantSubContextIterator.VcfTuple>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<PairedVariantSubContextIterator.VcfTuple>