244 lines
9.9 KiB
Java
Executable File
244 lines
9.9 KiB
Java
Executable File
/*
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* Copyright (c) 2009 The Broad Institute
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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 THE USE OR
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* 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.SAMRecord;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.walkers.DuplicateWalker;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.Pair;
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import org.broadinstitute.sting.utils.QualityUtils;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.utils.duplicates.DupUtils;
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import org.broadinstitute.sting.utils.duplicates.DuplicateComp;
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import java.io.PrintStream;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Set;
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class MismatchCounter {
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long nObs = 0;
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long nMismatches = 0;
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public void inc(long incNObs, long incNMismatches) {
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nObs += incNObs;
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nMismatches += incNMismatches;
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}
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public void inc(boolean mismatchP) {
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inc(1, mismatchP ? 1 : 0);
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}
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public double mismatchRate() {
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return (double)nMismatches / nObs;
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}
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public byte empiricalQualScore() {
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return QualityUtils.probToQual(1 - mismatchRate(), 0);
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}
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public String headerString() {
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return "mismatchRate\tempiricalQ\tnObs\tnMismatches";
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}
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public String toString() {
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return String.format("%.10f\t%d\t%d\t%6d", mismatchRate(), empiricalQualScore(), nObs, nMismatches);
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}
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}
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class QualityTracker {
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final private int MAX_QUAL_SCORE = 100;
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MismatchCounter[][] mismatchesByQ = new MismatchCounter[MAX_QUAL_SCORE][MAX_QUAL_SCORE];
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public QualityTracker() {
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for ( int i = 0; i < MAX_QUAL_SCORE; i++ ) {
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for ( int j = 0; j < MAX_QUAL_SCORE; j++ ) {
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mismatchesByQ[i][j] = new MismatchCounter();
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}
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}
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}
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public void inc(int b1Qi, int b2Qi, boolean mismatchP, boolean orderDependent) {
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int b1Q = orderDependent ? b1Qi : Math.max(b1Qi, b2Qi);
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int b2Q = orderDependent ? b2Qi : Math.min(b1Qi, b2Qi);
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if ( b1Q > MAX_QUAL_SCORE ) throw new RuntimeException("Unexpectedly large base quality " + b1Q);
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if ( b2Q > MAX_QUAL_SCORE ) throw new RuntimeException("Unexpectedly large base quality " + b2Q);
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mismatchesByQ[b1Q][b2Q].inc(mismatchP);
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}
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public void inc(DuplicateComp dc, boolean orderDependent) {
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inc(dc.getQLarger(), dc.getQSmaller(), dc.isMismatchP(), orderDependent);
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}
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public int probMismatchQ1Q2(int q1, int q2) {
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double e1 = 1 - QualityUtils.qualToProb(q1);
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double e2 = 1 - QualityUtils.qualToProb(q2);
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double eMM = e1 * (1 - e2) + (1 - e1) * e2 - 1/3 * e1 * e2;
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return QualityUtils.probToQual(1 - eMM, 0.0);
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}
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public void printToStream(PrintStream out, boolean filterUnobserved) {
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out.printf("Q1\tQ2\tQmin\t%s%n", mismatchesByQ[0][0].headerString());
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for ( int i = 0; i < MAX_QUAL_SCORE; i++ ) {
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for ( int j = 0; j < MAX_QUAL_SCORE; j++ ) {
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MismatchCounter mc = mismatchesByQ[i][j];
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//System.out.printf("MC = %s%n", mc);
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if ( filterUnobserved && mc.nObs == 0 )
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continue;
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out.printf("%d\t%d\t%d\t%s\t%n", i, j, probMismatchQ1Q2(i,j), mc.toString());
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}
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}
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}
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}
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public class DuplicateQualsWalker extends DuplicateWalker<List<DuplicateComp>, QualityTracker> {
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@Argument(fullName="filterUnobservedQuals", required=false, doc="Show only quality bins with at least one observation in the data")
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public boolean FILTER_UNOBSERVED_QUALS = false;
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@Argument(fullName="maxPairwiseCompsPerDupSet", required=false, doc="Maximumize number of pairwise comparisons to perform among duplicate read sets")
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public int MAX_PAIRSIZE_COMPS_PER_DUPLICATE_SET = 100;
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@Argument(fullName="combinedQuals", required=false, doc="Combine and assess pairwise base qualities")
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public boolean COMBINE_QUALS = false;
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@Argument(fullName="combineAllDups", required=false, doc="Combine and assess pairwise base qualities")
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public boolean COMBINE_ALL_DUPS = false;
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@Argument(fullName="orderDependent", required=false, doc="")
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public boolean orderDependent = false;
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@Argument(fullName="compareToUniqueReads", required=false, doc="If true, then we will compare only to unique (i.e., non-duplicated molecules) at the same duplicate site")
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public boolean compareToUniqueReads = false;
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@Argument(fullName="comparePairToSingleton", required=false, doc="If true, then we will compare a combined dup to a random other read in the duplicate set, not a combined pair itself")
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public boolean comparePairToSingleton = false;
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final boolean DEBUG = false;
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final private boolean ACTUALLY_DO_WORK = true;
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public void onTraversalDone(QualityTracker result) {
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result.printToStream(out, FILTER_UNOBSERVED_QUALS);
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}
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public QualityTracker reduceInit() {
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return new QualityTracker();
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}
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public QualityTracker reduce(List<DuplicateComp> dupComps, QualityTracker tracker) {
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for ( DuplicateComp dc : dupComps ) {
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tracker.inc(dc, orderDependent);
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}
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return tracker;
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}
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// Print out data for regression
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public List<DuplicateComp> map(GenomeLoc loc, AlignmentContext context, Set<List<SAMRecord>> readSets ) {
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//logger.info(String.format("%s has %d duplicates and %d non-duplicates", loc, duplicateReads.size(), uniqueReads.size()));
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List<DuplicateComp> pairwiseComps = new ArrayList<DuplicateComp>();
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// todo -- fixme -- the logic here is all wrong given new interface
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// if ( ! ACTUALLY_DO_WORK )
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// return pairwiseComps;
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//
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// if ( COMBINE_QUALS ) {
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// Pair<SAMRecord, SAMRecord> combinedReads = DupUtils.combinedReadPair( duplicateReads );
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// if ( combinedReads != null ) {
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// SAMRecord combined1 = combinedReads.first;
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// SAMRecord combined2 = combinedReads.second;
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//
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// if ( comparePairToSingleton )
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// pairwiseComps = addPairwiseMatches( pairwiseComps, combined1, duplicateReads.get(2), uniqueReads );
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// else
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// pairwiseComps = addPairwiseMatches( pairwiseComps, combined1, combined2, uniqueReads );
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// }
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// } else {
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// int nComparisons = 0;
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// for ( SAMRecord read1 : duplicateReads ) {
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// for ( SAMRecord read2 : duplicateReads ) {
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// if ( read1.hashCode() < read2.hashCode() && DupUtils.usableDuplicate(read1, read2) ) {
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// // the hashcode insures we don't do A vs. B and B vs. A
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// //System.out.printf("Comparing %s against %s%n", read1, read2);
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// nComparisons++;
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// pairwiseComps = addPairwiseMatches( pairwiseComps, read1, read2, uniqueReads );
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// if ( nComparisons > MAX_PAIRSIZE_COMPS_PER_DUPLICATE_SET )
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// break;
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// }
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// }
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// }
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// }
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return pairwiseComps;
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}
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private List<DuplicateComp> addPairwiseMatches(List<DuplicateComp> comps,
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SAMRecord read1, SAMRecord read2,
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List<SAMRecord> uniqueReads ) {
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if ( compareToUniqueReads ) {
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// we want to compare to a read in the unique read set
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if ( uniqueReads.size() > 0 ) { // there's actually something to compare to
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SAMRecord uniqueRead = uniqueReads.get(0); // might as well get the first one
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return pairwiseMatches(comps, read1, uniqueRead);
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} else {
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return comps;
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}
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} else {
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// default, just do read1 vs. read2
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return pairwiseMatches(comps, read1, read2);
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}
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}
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/**
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* Calculates the pairwise mismatches between reads read1 and read2 and adds the result to the comps list.
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* Doesn't contain any logic deciding what to compare, just does read1 and read2
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*
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* @param comps
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* @param read1
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* @param read2
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* @return
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*/
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private List<DuplicateComp> pairwiseMatches(List<DuplicateComp> comps, SAMRecord read1, SAMRecord read2 ) {
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byte[] read1Bases = read1.getReadBases();
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byte[] read1Quals = read1.getBaseQualities();
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byte[] read2Bases = read2.getReadBases();
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byte[] read2Quals = read2.getBaseQualities();
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for ( int i = 0; i < read1Bases.length; i++) {
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byte qual1 = read1Quals[i];
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byte qual2 = read2Quals[i];
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boolean mismatchP = ! BaseUtils.basesAreEqual(read1Bases[i], read2Bases[i]);
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DuplicateComp dc = new DuplicateComp(qual1, qual2, mismatchP);
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comps.add(dc);
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}
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return comps;
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}
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} |