Package picard.vcf
Class ByIntervalListVariantContextIterator
java.lang.Object
picard.vcf.ByIntervalListVariantContextIterator
- All Implemented Interfaces:
Iterator<htsjdk.variant.variantcontext.VariantContext>
public class ByIntervalListVariantContextIterator
extends Object
implements 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
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Constructor Summary
ConstructorsConstructorDescriptionByIntervalListVariantContextIterator
(htsjdk.variant.vcf.VCFFileReader reader, htsjdk.samtools.util.IntervalList intervals) -
Method Summary
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
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Constructor Details
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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.
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Method Details
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hasNext
public boolean hasNext() -
next
public htsjdk.variant.variantcontext.VariantContext next() -
remove
public void remove()
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