htsjdk.samtools.util

Class SamLocusIterator

java.lang.Object

htsjdk.samtools.util.AbstractLocusIterator<SamLocusIterator.RecordAndOffset,SamLocusIterator.LocusInfo>

htsjdk.samtools.util.SamLocusIterator

All Implemented Interfaces:

CloseableIterator<SamLocusIterator.LocusInfo>, java.io.Closeable, java.lang.AutoCloseable, java.lang.Iterable<SamLocusIterator.LocusInfo>, java.util.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().

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SamLocusIterator.LocusInfo The unit of iteration.
static class	SamLocusIterator.RecordAndOffset Implementation of AbstractRecordAndOffset class for SamLocusIterator.

Field Summary

Fields inherited from class htsjdk.samtools.util.AbstractLocusIterator

includeIndels

Constructor Summary

Constructors

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

Method Summary

Methods inherited from class htsjdk.samtools.util.AbstractLocusIterator

close, getCurrentInterval, getIntervals, getMappingQualityScoreCutoff, getMaxReadsToAccumulatePerLocus, getQualityScoreCutoff, getReferenceSequence, hasNext, isEmitUncoveredLoci, isIncludeIndels, isIncludeNonPfReads, iterator, next, remove, setEmitUncoveredLoci, setIncludeIndels, setIncludeNonPfReads, setMappingQualityScoreCutoff, setMaxReadsToAccumulatePerLocus, setQualityScoreCutoff, setSamFilters, startWithInsertion

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

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

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 sorted

intervalList - 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.

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 sorted

intervalList - 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.