public class EdgeReadIterator extends AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>
includeIndels
Constructor and Description |
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EdgeReadIterator(SamReader samReader)
Prepare to iterate through the given SAM records, skipping non-primary alignments.
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EdgeReadIterator(SamReader samReader,
IntervalList intervalList)
Prepare to iterate through the given SAM records, skipping non-primary alignments.
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EdgeReadIterator(SamReader samReader,
IntervalList intervalList,
boolean useIndex)
Prepare to iterate through the given SAM records, skipping non-primary alignments
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Modifier and Type | Method and Description |
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void |
setEmitUncoveredLoci(boolean emitUncoveredLoci)
For correct work of
EdgeReadIterator value emitUncoveredLoci must be true. |
void |
setIncludeIndels(boolean includeIndels) |
void |
setMaxReadsToAccumulatePerLocus(int maxReadsToAccumulatePerLocus)
This method isn't supported in current implementation.
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void |
setQualityScoreCutoff(int qualityScoreCutoff)
This method isn't supported in current implementation.
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close, getCurrentInterval, getIntervals, getMappingQualityScoreCutoff, getMaxReadsToAccumulatePerLocus, getQualityScoreCutoff, getReferenceSequence, hasNext, isEmitUncoveredLoci, isIncludeIndels, isIncludeNonPfReads, iterator, next, remove, setIncludeNonPfReads, setMappingQualityScoreCutoff, setSamFilters, startWithInsertion
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
stream, toList
public EdgeReadIterator(SamReader samReader)
samReader
- must be coordinate sortedpublic EdgeReadIterator(SamReader samReader, IntervalList intervalList)
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.public EdgeReadIterator(SamReader samReader, IntervalList intervalList, boolean useIndex)
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.public void setMaxReadsToAccumulatePerLocus(int maxReadsToAccumulatePerLocus)
setMaxReadsToAccumulatePerLocus
in class AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>
maxReadsToAccumulatePerLocus
- maximum number of RecordAndOffset
objects to store for
one loci in reference sequence.public void setQualityScoreCutoff(int qualityScoreCutoff)
setQualityScoreCutoff
in class AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>
qualityScoreCutoff
- the minimum base quality to include in AbstractLocusInfo
.public void setEmitUncoveredLoci(boolean emitUncoveredLoci)
EdgeReadIterator
value emitUncoveredLoci
must be true.setEmitUncoveredLoci
in class AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>
emitUncoveredLoci
- if false, iterator will skip uncovered loci in reference sequence, otherwise
empty AbstractLocusInfo
will be created for each loci.public void setIncludeIndels(boolean includeIndels)
setIncludeIndels
in class AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>