picard.vcf

Class ByIntervalListVariantContextIterator

java.lang.Object

picard.vcf.ByIntervalListVariantContextIterator

All Implemented Interfaces:

java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>

public class ByIntervalListVariantContextIterator
extends java.lang.Object
implements java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>

Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals. //TODO Currently this uses the VCFFileReader.query method - could be useful to make a version of this iterator that uses the .iterator method

Constructor Summary

Constructors

Constructor and Description
ByIntervalListVariantContextIterator(htsjdk.variant.vcf.VCFFileReader reader, htsjdk.samtools.util.IntervalList intervals)

Method Summary

Modifier and Type	Method and Description
boolean	hasNext()
htsjdk.variant.variantcontext.VariantContext	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

ByIntervalListVariantContextIterator

public ByIntervalListVariantContextIterator(htsjdk.variant.vcf.VCFFileReader reader,
                                            htsjdk.samtools.util.IntervalList intervals)

Parameters:

reader - the source of variants.

intervals - the intervals to which to restrict variants.

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>

next

public htsjdk.variant.variantcontext.VariantContext next()

Specified by:

next in interface java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<htsjdk.variant.variantcontext.VariantContext>