Package htsjdk.samtools.util
Class EdgeReadIterator
- java.lang.Object
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- htsjdk.samtools.util.AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>
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- htsjdk.samtools.util.EdgeReadIterator
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- All Implemented Interfaces:
CloseableIterator<AbstractLocusInfo<EdgingRecordAndOffset>>
,Closeable
,AutoCloseable
,Iterable<AbstractLocusInfo<EdgingRecordAndOffset>>
,Iterator<AbstractLocusInfo<EdgingRecordAndOffset>>
public class EdgeReadIterator extends AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>
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(). Difference from SamLocusIterator is that this implementation accumulates data only about start and end of alignment blocks from reads, not about each aligned base.
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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 EdgeReadIterator(SamReader samReader)
Prepare to iterate through the given SAM records, skipping non-primary alignments.EdgeReadIterator(SamReader samReader, IntervalList intervalList)
Prepare to iterate through the given SAM records, skipping non-primary alignments.EdgeReadIterator(SamReader samReader, IntervalList intervalList, boolean useIndex)
Prepare to iterate through the given SAM records, skipping non-primary alignments
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
setEmitUncoveredLoci(boolean emitUncoveredLoci)
For correct work ofEdgeReadIterator
valueemitUncoveredLoci
must be true.void
setIncludeIndels(boolean includeIndels)
void
setMaxReadsToAccumulatePerLocus(int maxReadsToAccumulatePerLocus)
This method isn't supported in current implementation.void
setQualityScoreCutoff(int qualityScoreCutoff)
This method isn't supported in current implementation.-
Methods inherited from class htsjdk.samtools.util.AbstractLocusIterator
close, getCurrentInterval, getHeader, getIntervals, getMappingQualityScoreCutoff, getMaxReadsToAccumulatePerLocus, getQualityScoreCutoff, getReferenceSequence, hasNext, isEmitUncoveredLoci, isIncludeIndels, isIncludeNonPfReads, iterator, next, remove, setIncludeNonPfReads, setMappingQualityScoreCutoff, 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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EdgeReadIterator
public EdgeReadIterator(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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EdgeReadIterator
public EdgeReadIterator(SamReader samReader, IntervalList intervalList)
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.
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EdgeReadIterator
public EdgeReadIterator(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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Method Detail
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setMaxReadsToAccumulatePerLocus
public void setMaxReadsToAccumulatePerLocus(int maxReadsToAccumulatePerLocus)
This method isn't supported in current implementation.- Overrides:
setMaxReadsToAccumulatePerLocus
in classAbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>
- Parameters:
maxReadsToAccumulatePerLocus
- maximum number ofRecordAndOffset
objects to store for one loci in reference sequence.
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setQualityScoreCutoff
public void setQualityScoreCutoff(int qualityScoreCutoff)
This method isn't supported in current implementation.- Overrides:
setQualityScoreCutoff
in classAbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>
- Parameters:
qualityScoreCutoff
- the minimum base quality to include inAbstractLocusInfo
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setEmitUncoveredLoci
public void setEmitUncoveredLoci(boolean emitUncoveredLoci)
For correct work ofEdgeReadIterator
valueemitUncoveredLoci
must be true.- Overrides:
setEmitUncoveredLoci
in classAbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>
- Parameters:
emitUncoveredLoci
- if false, iterator will skip uncovered loci in reference sequence, otherwise emptyAbstractLocusInfo
will be created for each loci.
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setIncludeIndels
public void setIncludeIndels(boolean includeIndels)
- Overrides:
setIncludeIndels
in classAbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>
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