Package htsjdk.samtools.util

Class EdgeReadIterator

java.lang.Object

htsjdk.samtools.util.AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>

htsjdk.samtools.util.EdgeReadIterator

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.

Field Summary

Fields inherited from class htsjdk.samtools.util.AbstractLocusIterator

includeIndels

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

Method Summary

Modifier and Type	Method	Description
protected boolean	advanceCurrentIntervalAndCheckIfIntervalContainsRead(SAMRecord rec)	This function updates currentInterval according to the position of the record that it is presented and determines if the current read is fully contained in the currentInterval.
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.
void	setQualityScoreCutoff(int qualityScoreCutoff)	This method isn't supported in current implementation.

Methods inherited from class htsjdk.samtools.util.AbstractLocusIterator

close, getHeader, getIntervals, getMappingQualityScoreCutoff, getMaxReadsToAccumulatePerLocus, getQualityScoreCutoff, getReferenceSequence, hasNext, isEmitUncoveredLoci, isIncludeIndels, isIncludeNonPfReads, iterator, next, remove, setIncludeNonPfReads, setMappingQualityScoreCutoff, setSamFilters, startWithInsertion

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Details

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

EdgeReadIterator

public EdgeReadIterator(SamReader samReader,
 IntervalList intervalList)

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 be coordinated sorted by this class.

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 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 be coordinated sorted here.

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.

Method Details

advanceCurrentIntervalAndCheckIfIntervalContainsRead

protected boolean advanceCurrentIntervalAndCheckIfIntervalContainsRead(SAMRecord rec)

This function updates currentInterval according to the position of the record that it is presented and determines if the current read is fully contained in the currentInterval.

Parameters:

rec - The record we want to consider

Returns:

True, if rec is fully contained in the current interval, otherwise false

setMaxReadsToAccumulatePerLocus

public void setMaxReadsToAccumulatePerLocus(int maxReadsToAccumulatePerLocus)

This method isn't supported in current implementation.

Overrides:

setMaxReadsToAccumulatePerLocus in class AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>

Parameters:

maxReadsToAccumulatePerLocus - maximum number of RecordAndOffset objects to store for one loci in reference sequence.

setQualityScoreCutoff

public void setQualityScoreCutoff(int qualityScoreCutoff)

This method isn't supported in current implementation.

Overrides:

setQualityScoreCutoff in class AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>

Parameters:

qualityScoreCutoff - the minimum base quality to include in AbstractLocusInfo.

setEmitUncoveredLoci

public void setEmitUncoveredLoci(boolean emitUncoveredLoci)

For correct work of EdgeReadIterator value emitUncoveredLoci must be true.

Overrides:

setEmitUncoveredLoci in class AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>

Parameters:

emitUncoveredLoci - if false, iterator will skip uncovered loci in reference sequence, otherwise empty AbstractLocusInfo will be created for each loci.

setIncludeIndels

public void setIncludeIndels(boolean includeIndels)

Overrides:

setIncludeIndels in class AbstractLocusIterator<EdgingRecordAndOffset,AbstractLocusInfo<EdgingRecordAndOffset>>