Package htsjdk.samtools.reference
Class SamLocusAndReferenceIterator
- java.lang.Object
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- htsjdk.samtools.util.IterableOnceIterator<SamLocusAndReferenceIterator.SAMLocusAndReference>
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- htsjdk.samtools.reference.SamLocusAndReferenceIterator
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- 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 Classes Modifier and Type Class Description static class
SamLocusAndReferenceIterator.SAMLocusAndReference
Small class to hold together aSamLocusIterator.LocusInfo
and the reference base over that locus.
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Constructor Summary
Constructors Constructor Description SamLocusAndReferenceIterator(ReferenceSequenceFileWalker referenceFile, SamLocusIterator locusIterator)
Constructor that takes aReferenceSequenceFile
and aSamLocusIterator
.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
hasNext()
SamLocusAndReferenceIterator.SAMLocusAndReference
next()
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Methods inherited from class htsjdk.samtools.util.IterableOnceIterator
close, iterator, remove
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Detail
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SamLocusAndReferenceIterator
public SamLocusAndReferenceIterator(ReferenceSequenceFileWalker referenceFile, SamLocusIterator locusIterator) throws IllegalArgumentException
Constructor that takes aReferenceSequenceFile
and aSamLocusIterator
. The inputs must have equalSAMSequenceDictionary
s and anIllegalArgumentException
will be thrown otherwise.- Parameters:
referenceFile
-locusIterator
-- Throws:
IllegalArgumentException
- if arguments have non-equalSAMSequenceDictionary
s
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Method Detail
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hasNext
public boolean hasNext()
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next
public SamLocusAndReferenceIterator.SAMLocusAndReference next()
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