public class SamLocusIterator extends AbstractLocusIterator<SamLocusIterator.RecordAndOffset,SamLocusIterator.LocusInfo>
Modifier and Type | Class and Description |
---|---|
static class |
SamLocusIterator.LocusInfo
The unit of iteration.
|
static class |
SamLocusIterator.RecordAndOffset
Implementation of
AbstractRecordAndOffset class for SamLocusIterator . |
includeIndels
Constructor and 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
|
close, getCurrentInterval, getIntervals, getMappingQualityScoreCutoff, getMaxReadsToAccumulatePerLocus, getQualityScoreCutoff, getReferenceSequence, hasNext, isEmitUncoveredLoci, isIncludeIndels, isIncludeNonPfReads, iterator, next, remove, setEmitUncoveredLoci, setIncludeIndels, setIncludeNonPfReads, setMappingQualityScoreCutoff, setMaxReadsToAccumulatePerLocus, setQualityScoreCutoff, setSamFilters, startWithInsertion
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
stream, toList
public SamLocusIterator(SamReader samReader)
samReader
- must be coordinate sortedpublic SamLocusIterator(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 SamLocusIterator(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.