Package htsjdk.samtools.util
Class SamLocusIterator
- java.lang.Object
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- htsjdk.samtools.util.AbstractLocusIterator<SamLocusIterator.RecordAndOffset,SamLocusIterator.LocusInfo>
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- htsjdk.samtools.util.SamLocusIterator
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- All Implemented Interfaces:
CloseableIterator<SamLocusIterator.LocusInfo>
,Closeable
,AutoCloseable
,Iterable<SamLocusIterator.LocusInfo>
,Iterator<SamLocusIterator.LocusInfo>
public class SamLocusIterator extends AbstractLocusIterator<SamLocusIterator.RecordAndOffset,SamLocusIterator.LocusInfo>
Iterator that traverses a SAM File, accumulating information on a per-locus basis. Optionally takes a target interval list, in which case the loci returned are the ones covered by the interval list. If no target interval list, whatever loci are covered by the input reads are returned. By default duplicate reads and non-primary alignments are filtered out. Filtering may be changed via setSamFilters().
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SamLocusIterator.LocusInfo
The unit of iteration.static class
SamLocusIterator.RecordAndOffset
Implementation ofAbstractRecordAndOffset
class forSamLocusIterator
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Field Summary
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Fields inherited from class htsjdk.samtools.util.AbstractLocusIterator
includeIndels
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Constructor Summary
Constructors Constructor Description SamLocusIterator(SamReader samReader)
Prepare to iterate through the given SAM records, skipping non-primary alignments.SamLocusIterator(SamReader samReader, IntervalList intervalList)
Prepare to iterate through the given SAM records, skipping non-primary alignments.SamLocusIterator(SamReader samReader, IntervalList intervalList, boolean useIndex)
Prepare to iterate through the given SAM records, skipping non-primary alignments
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Method Summary
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Methods inherited from class htsjdk.samtools.util.AbstractLocusIterator
close, getCurrentInterval, getHeader, getIntervals, getMappingQualityScoreCutoff, getMaxReadsToAccumulatePerLocus, getQualityScoreCutoff, getReferenceSequence, hasNext, isEmitUncoveredLoci, isIncludeIndels, isIncludeNonPfReads, iterator, next, remove, setEmitUncoveredLoci, setIncludeIndels, setIncludeNonPfReads, setMappingQualityScoreCutoff, setMaxReadsToAccumulatePerLocus, setQualityScoreCutoff, setSamFilters, startWithInsertion
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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 htsjdk.samtools.util.CloseableIterator
stream, toList
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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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SamLocusIterator
public SamLocusIterator(SamReader samReader)
Prepare to iterate through the given SAM records, skipping non-primary alignments. Do not use BAM index even if available.- Parameters:
samReader
- must be coordinate sorted
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SamLocusIterator
public SamLocusIterator(SamReader samReader, IntervalList intervalList)
Prepare to iterate through the given SAM records, skipping non-primary alignments. Do not use BAM index even if available.- Parameters:
samReader
- must be coordinate sortedintervalList
- Either the list of desired intervals, or null. Note that if an intervalList is passed in that is not coordinate sorted, it will eventually be coordinated sorted by this class.
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SamLocusIterator
public SamLocusIterator(SamReader samReader, IntervalList intervalList, boolean useIndex)
Prepare to iterate through the given SAM records, skipping non-primary alignments- Parameters:
samReader
- must be coordinate sortedintervalList
- Either the list of desired intervals, or null. Note that if an intervalList is passed in that is not coordinate sorted, it will eventually be coordinated sorted by this class.useIndex
- If true, do indexed lookup to improve performance. Not relevant if intervalList == null. It is no longer the case the useIndex==true can make performance worse. It should always perform at least as well as useIndex==false, and generally will be much faster.
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