Package htsjdk.samtools.reference
Class SamLocusAndReferenceIterator
java.lang.Object
htsjdk.samtools.util.IterableOnceIterator<SamLocusAndReferenceIterator.SAMLocusAndReference>
htsjdk.samtools.reference.SamLocusAndReferenceIterator
- All Implemented Interfaces:
Closeable,AutoCloseable,Iterable<SamLocusAndReferenceIterator.SAMLocusAndReference>,Iterator<SamLocusAndReferenceIterator.SAMLocusAndReference>
public class SamLocusAndReferenceIterator
extends IterableOnceIterator<SamLocusAndReferenceIterator.SAMLocusAndReference>
Iterator that traverses a SAM File and a ReferenceFile, accumulating information on a per-locus basis.
Only loci that are covered by the input reads are returned.
Duplicate reads and non-primary alignments are filtered out.
Iterator element holds both pileup (in the form of a LocusInfo object) and the reference base
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic classSmall class to hold together aSamLocusIterator.LocusInfoand the reference base over that locus. -
Constructor Summary
ConstructorsConstructorDescriptionSamLocusAndReferenceIterator(ReferenceSequenceFileWalker referenceFile, SamLocusIterator locusIterator) Constructor that takes aReferenceSequenceFileand aSamLocusIterator. -
Method Summary
Methods inherited from class htsjdk.samtools.util.IterableOnceIterator
close, iterator, removeMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface java.lang.Iterable
forEach, spliteratorMethods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Details
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SamLocusAndReferenceIterator
public SamLocusAndReferenceIterator(ReferenceSequenceFileWalker referenceFile, SamLocusIterator locusIterator) throws IllegalArgumentException Constructor that takes aReferenceSequenceFileand aSamLocusIterator. The inputs must have equalSAMSequenceDictionarys and anIllegalArgumentExceptionwill be thrown otherwise.- Parameters:
referenceFile-locusIterator-- Throws:
IllegalArgumentException- if arguments have non-equalSAMSequenceDictionarys
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Method Details
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hasNext
public boolean hasNext() -
next
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