131 lines
5.0 KiB
Java
Executable File
131 lines
5.0 KiB
Java
Executable File
/*
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* Copyright (c) 2010.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.walkers;
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import net.sf.samtools.*;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.*;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.filters.BadMateFilter;
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import org.broadinstitute.sting.utils.*;
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import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
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import org.broadinstitute.sting.utils.sam.ReadUtils;
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import org.broadinstitute.sting.commandline.Argument;
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import java.io.File;
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import java.util.*;
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@By(DataSource.READS)
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// walker to count realigned reads
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public class RealignedReadCounter extends ReadWalker<Integer, Integer> {
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public static final String ORIGINAL_CIGAR_TAG = "OC";
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public static final String ORIGINAL_POSITION_TAG = "OP";
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@Argument(fullName="targetIntervals", shortName="targetIntervals", doc="intervals file output from RealignerTargetCreator", required=true)
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protected String intervalsFile = null;
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// the intervals input by the user
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private Iterator<GenomeLoc> intervals = null;
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// the current interval in the list
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private GenomeLoc currentInterval = null;
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private long updatedIntervals = 0, updatedReads = 0;
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private boolean intervalWasUpdated = false;
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public void initialize() {
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// prepare to read intervals one-by-one, as needed (assuming they are sorted).
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intervals = new IntervalFileMergingIterator( new File(intervalsFile), IntervalMergingRule.OVERLAPPING_ONLY );
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currentInterval = intervals.hasNext() ? intervals.next() : null;
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}
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public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
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if ( currentInterval == null ) {
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return 0;
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}
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GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read);
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// hack to get around unmapped reads having screwy locations
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if ( readLoc.getStop() == 0 )
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readLoc = GenomeLocParser.createGenomeLoc(readLoc.getContigIndex(), readLoc.getStart(), readLoc.getStart());
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if ( readLoc.isBefore(currentInterval) || ReadUtils.is454Read(read) )
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return 0;
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if ( readLoc.overlapsP(currentInterval) ) {
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if ( doNotTryToClean(read) )
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return 0;
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if ( read.getAttribute(ORIGINAL_CIGAR_TAG) != null ) {
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String newCigar = (String)read.getAttribute(ORIGINAL_CIGAR_TAG);
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// deal with an old bug
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if ( read.getCigar().toString().equals(newCigar) ) {
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//System.out.println(currentInterval + ": " + read.getReadName() + " " + read.getCigarString() + " " + newCigar);
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return 0;
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}
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if ( !intervalWasUpdated ) {
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intervalWasUpdated = true;
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updatedIntervals++;
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}
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updatedReads++;
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}
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} else {
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do {
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intervalWasUpdated = false;
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currentInterval = intervals.hasNext() ? intervals.next() : null;
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} while ( currentInterval != null && currentInterval.isBefore(readLoc) );
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}
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return 0;
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}
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private boolean doNotTryToClean(SAMRecord read) {
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return read.getReadUnmappedFlag() ||
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read.getNotPrimaryAlignmentFlag() ||
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read.getReadFailsVendorQualityCheckFlag() ||
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read.getMappingQuality() == 0 ||
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read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
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(BadMateFilter.hasBadMate(read));
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}
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public Integer reduceInit() {
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return 0;
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}
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public Integer reduce(Integer value, Integer sum) {
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return sum + value;
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}
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public void onTraversalDone(Integer result) {
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System.out.println(updatedIntervals + " intervals were updated");
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System.out.println(updatedReads + " reads were updated");
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}
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}
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