/*
* The MIT License
*
* Copyright (c) 2014 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.sam.markduplicates.util;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMUtils;
import htsjdk.samtools.util.SamRecordWithOrdinal;
import picard.PicardException;
import java.util.List;
import java.util.Set;
/**
* A class to store individual records for MarkDuplicatesWithMateCigar. This aids in comparing records to determine which need to
* be compared when we mark duplicates. We also store the original SAMRecord and its ordinal in the input file (in SamRecordWithOrdinal) to
* access optional tags (mate cigar) and other information.
*/
public class ReadEndsForMateCigar extends ReadEnds {
// to see if either end is unmapped
byte hasUnmapped = 0;
// we need this reference so we can access the mate cigar among other things
public SamRecordWithOrdinal samRecordWithOrdinal = null;
/**
* Physical locations used for optical duplicate tracking. This is only stored for paired end reads where both ends are mapped,
* and when we see the first mate.
*/
private PhysicalLocationForMateCigarSet locationSet = null;
/** Builds a read ends object that represents a single read. */
public ReadEndsForMateCigar(final SAMFileHeader header, final SamRecordWithOrdinal samRecordWithOrdinal,
final OpticalDuplicateFinder opticalDuplicateFinder, final short libraryId) {
this.readGroup = -1;
this.tile = -1;
this.x = this.y = -1;
this.read2ReferenceIndex = this.read2Coordinate = -1;
this.hasUnmapped = 0;
this.samRecordWithOrdinal = samRecordWithOrdinal;
final SAMRecord record = this.samRecordWithOrdinal.getRecord();
this.read1ReferenceIndex = record.getReferenceIndex();
this.read1Coordinate = record.getReadNegativeStrandFlag() ? record.getUnclippedEnd() : record.getUnclippedStart();
if (record.getReadUnmappedFlag()) {
throw new PicardException("Found an unexpected unmapped read");
}
if (record.getReadPairedFlag() && !record.getReadUnmappedFlag() && !record.getMateUnmappedFlag()) {
this.read2ReferenceIndex = record.getMateReferenceIndex();
this.read2Coordinate = record.getMateNegativeStrandFlag() ? SAMUtils.getMateUnclippedEnd(record) : SAMUtils.getMateUnclippedStart(record);
// set orientation
this.orientation = ReadEnds.getOrientationByte(record.getReadNegativeStrandFlag(), record.getMateNegativeStrandFlag());
// Set orientationForOpticalDuplicates, which always goes by the first then the second end for the strands. NB: must do this
// before updating the orientation later.
if (record.getReadPairedFlag()) {
if (record.getFirstOfPairFlag()) {
this.orientationForOpticalDuplicates = ReadEnds.getOrientationByte(record.getReadNegativeStrandFlag(), record.getMateNegativeStrandFlag());
} else {
this.orientationForOpticalDuplicates = ReadEnds.getOrientationByte(record.getMateNegativeStrandFlag(), record.getReadNegativeStrandFlag());
}
}
} else {
this.orientation = record.getReadNegativeStrandFlag() ? ReadEndsForMateCigar.R : ReadEndsForMateCigar.F;
}
// Fill in the library ID
this.libraryId = libraryId;
// Is this unmapped or its mate?
if (record.getReadUnmappedFlag() || (record.getReadPairedFlag() && record.getMateUnmappedFlag())) {
this.hasUnmapped = 1;
}
// Fill in the location information for optical duplicates
if (opticalDuplicateFinder.addLocationInformation(record.getReadName(), this)) {
// calculate the RG number (nth in list)
// NB: could this be faster if we used a hash?
this.readGroup = 0;
final String rg = (String) record.getAttribute("RG");
final List<SAMReadGroupRecord> readGroups = header.getReadGroups();
if (rg != null && readGroups != null) {
for (final SAMReadGroupRecord readGroup : readGroups) {
if (readGroup.getReadGroupId().equals(rg)) break;
else this.readGroup++;
}
}
}
}
/** Creates a shallow copy from the "other" */
public ReadEndsForMateCigar(final ReadEndsForMateCigar other, final SamRecordWithOrdinal samRecordWithOrdinal) {
this.readGroup = other.readGroup;
this.tile = other.tile;
this.x = other.x;
this.y = other.y;
this.read1ReferenceIndex = other.read1ReferenceIndex;
this.read1Coordinate = other.read1Coordinate;
this.read2ReferenceIndex = other.read2ReferenceIndex;
this.read2Coordinate = other.read2Coordinate;
this.hasUnmapped = other.hasUnmapped;
this.samRecordWithOrdinal = samRecordWithOrdinal;
this.orientation = other.orientation;
this.libraryId = other.libraryId;
}
/** A number of convenience functions */
public SamRecordWithOrdinal getSamRecordIndex() { return this.samRecordWithOrdinal; }
public SAMRecord getRecord() { return this.samRecordWithOrdinal.getRecord(); }
public String getRecordReadName() { return this.samRecordWithOrdinal.getRecord().getReadName(); }
@Override
public boolean isPaired() { return this.getRecord().getReadPairedFlag(); }
/** Gets the read ends for optical duplicate tracking */
public Set<ReadEnds> getReadEndSetForOpticalDuplicates() {
if (null == this.locationSet) throw new PicardException("Already called getReadEndSetForOpticalDuplicates");
final Set<ReadEnds> locationSet = this.locationSet.getReadEnds();
this.locationSet = null;
return locationSet;
}
public PhysicalLocationForMateCigarSet getLocationSet() {
return this.locationSet;
}
public PhysicalLocationForMateCigarSet removeLocationSet() {
final PhysicalLocationForMateCigarSet locationSet = this.locationSet;
this.locationSet = null;
return locationSet;
}
public void setLocationSet(final PhysicalLocationForMateCigarSet locationSet) {
this.locationSet = locationSet;
}
}