/*
* The MIT License
*
* Copyright (c) 2012 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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* THE SOFTWARE.
*/
package picard.sam;
import htsjdk.samtools.SAMUtils;
import picard.sam.HitsForInsert.NumPrimaryAlignmentState;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
/**
* This strategy was designed for TopHat output, but could be of general utility. It picks the alignment with best MAPQ.
* If paired-end, it is the alignment in which the sum of the MAPQs of both ends is the best. In case of ties, one
* is selected arbitrarily. This strategy expects pair-aware alignments, with the corresponding alignment for each
* mate of the pair correlated by HI (hit index) tag. If the aligner has set a pair of alignments as primary, this
* is used (assuming one of those alignments is not filtered out). Otherwise the alignment pair with best MapQ is
* selected.
*/
public class BestMapqPrimaryAlignmentSelectionStrategy implements PrimaryAlignmentSelectionStrategy {
// Give random number generator a seed so results are repeatable. Used to pick a primary alignment from
// multiple alignments with equal mapping quality.
private final Random random = new Random(1);
/**
* Primary alignment was filtered out. Need to select a new one.
*/
public void pickPrimaryAlignment(final HitsForInsert hits) {
if (hits.numHits() == 0) throw new IllegalArgumentException("No alignments to pick from");
hits.coordinateByHitIndex();
// See if primary alignment is not already unambiguously determined.
final NumPrimaryAlignmentState firstEndAlignmentState = hits.tallyPrimaryAlignments(true);
final NumPrimaryAlignmentState secondEndAlignmentState = hits.tallyPrimaryAlignments(false);
if ((firstEndAlignmentState == NumPrimaryAlignmentState.NONE && secondEndAlignmentState == NumPrimaryAlignmentState.NONE) ||
firstEndAlignmentState == NumPrimaryAlignmentState.MORE_THAN_ONE ||
secondEndAlignmentState == NumPrimaryAlignmentState.MORE_THAN_ONE) {
// Need to use selected strategy for picking primary.
// Find all the hits with the best MAPQ.
final List<Integer> primaryAlignmentIndices = new ArrayList<Integer>(hits.numHits());
int bestMapQ = -1;
for (int i = 0; i < hits.numHits(); ++i) {
final int firstEndMapq;
if (hits.getFirstOfPair(i) != null) {
firstEndMapq = hits.getFirstOfPair(i).getMappingQuality();
} else {
firstEndMapq = 0;
}
final int secondEndMapq;
if (hits.getSecondOfPair(i) != null) {
secondEndMapq = hits.getSecondOfPair(i).getMappingQuality();
} else {
secondEndMapq = 0;
}
int thisMapQ = SAMUtils.combineMapqs(firstEndMapq, secondEndMapq);
if (thisMapQ > bestMapQ) {
bestMapQ = thisMapQ;
primaryAlignmentIndices.clear();
}
if (thisMapQ == bestMapQ) primaryAlignmentIndices.add(i);
}
// Of all the hits with the best MAPQ, randomly select one to be primary.
final int primaryAlignmentIndex;
if (primaryAlignmentIndices.size() == 1) primaryAlignmentIndex = primaryAlignmentIndices.get(0);
else if (primaryAlignmentIndices.size() > 1) primaryAlignmentIndex =
primaryAlignmentIndices.get(random.nextInt(primaryAlignmentIndices.size()));
else throw new IllegalStateException("Never found a best MAPQ -- should never happen");
hits.setPrimaryAlignment(primaryAlignmentIndex);
}
}
}