/*
* 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
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package picard.sam;
import htsjdk.samtools.AlignmentBlock;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.CoordMath;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
/**
* When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps
* the earliest base in the read. This implementation only works for fragments, not for pairs.
* If there are multiple alignments that all start mapping at the same offest in the read, pick the one with the best
* MAPQ. If there are multiple alignments that have the earliest mapping and that have the same MAPQ, pick one randomly.
*/
public class EarliestFragmentPrimaryAlignmentSelectionStrategy 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);
public void pickPrimaryAlignment(final HitsForInsert hitsForInsert) {
if (hitsForInsert.numHits() == 0) throw new IllegalArgumentException("No alignments to pick from");
// Gather the earliest alignment(s) with best MAPQ
final List<Integer> earliestAlignments = new ArrayList<Integer>();
int earliestMappedBase = Integer.MAX_VALUE;
int bestMapQ = -1;
for (int i = 0; i < hitsForInsert.numHits(); ++i) {
final SAMRecord rec = hitsForInsert.getFragment(i);
if (rec.getReadUnmappedFlag()) continue;
final int thisFirstMappedBase = getIndexOfFirstAlignedBase(rec);
final int thisMapQ = rec.getMappingQuality();
if (thisFirstMappedBase < earliestMappedBase ||
(thisFirstMappedBase == earliestMappedBase && thisMapQ > bestMapQ)) {
earliestAlignments.clear();
earliestAlignments.add(i);
earliestMappedBase = thisFirstMappedBase;
bestMapQ = thisMapQ;
} else if (thisFirstMappedBase == earliestMappedBase && thisMapQ == bestMapQ) {
earliestAlignments.add(i);
} // else it is not the earliest or the best so skip it.
}
if (earliestAlignments.size() == 1) {
// If only one best, pick it.
hitsForInsert.setPrimaryAlignment(earliestAlignments.get(0));
} else {
// Arbitrarily select one of the best
hitsForInsert.setPrimaryAlignment(earliestAlignments.get(random.nextInt(earliestAlignments.size())));
}
}
/**
* Returns 1-based index of first base in read that corresponds to M in CIGAR string.
* Note that first is relative to 5' end, so that for reverse-strand alignment, the index of
* the last base aligned is computed relative to the end of the read.
*/
int getIndexOfFirstAlignedBase(final SAMRecord rec) {
final List<AlignmentBlock> alignmentBlocks = rec.getAlignmentBlocks();
if (rec.getReadNegativeStrandFlag()) {
final AlignmentBlock alignmentBlock = alignmentBlocks.get(alignmentBlocks.size() - 1);
return rec.getReadLength() - CoordMath.getEnd(alignmentBlock.getReadStart(), alignmentBlock.getLength()) + 1;
} else {
return alignmentBlocks.get(0).getReadStart();
}
}
}