org.broadinstitute.hellbender.utils.read.mergealignment.BestEndMapqPrimaryAlignmentStrategy Maven / Gradle / Ivy
package org.broadinstitute.hellbender.utils.read.mergealignment;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMUtils;
import java.io.Serializable;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import java.util.Random;
/**
* For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and
* make that the primary. The primary alignments are then correlated so that their mate info points to each
* other, but all non-primary alignments are uncorrelated.
*/
public final class BestEndMapqPrimaryAlignmentStrategy implements PrimaryAlignmentSelectionStrategy {
private static final MapqComparator MAPQ_COMPARATOR = new MapqComparator();
// 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.
*/
@Override
public void pickPrimaryAlignment(final HitsForInsert hits) {
if (hits.numHits() == 0) throw new IllegalArgumentException("No alignments to pick from");
Collections.sort(hits.firstOfPairOrFragment, MAPQ_COMPARATOR);
Collections.sort(hits.secondOfPair, MAPQ_COMPARATOR);
randomlySelectPrimaryFromBest(hits.firstOfPairOrFragment);
randomlySelectPrimaryFromBest(hits.secondOfPair);
hits.setPrimaryAlignment(0);
if (!hits.isPaired()) return;
// For non-primary alignments, de-correlate them so that the mate fields don't point at some
// arbitrary alignment for the other end.
// No non-primary alignments for one of the ends so nothing to do.
if (hits.firstOfPairOrFragment.size() <= 1 || hits.secondOfPair.size() <= 1) return;
final int amountToSlide = hits.firstOfPairOrFragment.size() - 1;
for (int i = 0; i < amountToSlide; ++i) {
hits.secondOfPair.add(1, null);
}
}
/**
* Randomly picks one of the best alignments and puts it into the 0th slot of the list.
* @param recs List of alignments sorted in descending order of alignment quality.
*/
private void randomlySelectPrimaryFromBest(List recs) {
if (recs.isEmpty()) return;
final int bestMapq = recs.get(0).getMappingQuality();
int i;
for (i = 1; i < recs.size() && recs.get(i).getMappingQuality() == bestMapq; ++i) {
}
final int bestIndex = random.nextInt(i);
if (bestIndex == 0) return;
final SAMRecord tmp = recs.get(0);
recs.set(0, recs.get(bestIndex));
recs.set(bestIndex, tmp);
}
// Sorts in descending order, but 255 is considered > 0 but < 1, and unmapped is worst of all
private static class MapqComparator implements Comparator, Serializable {
private static final long serialVersionUID = 6763153425070516820L;
@Override
public int compare(final SAMRecord rec1, final SAMRecord rec2) {
if (rec1.getReadUnmappedFlag()) {
if (rec2.getReadUnmappedFlag()) return 0;
else return 1;
} else if (rec2.getReadUnmappedFlag()) {
return -1;
}
return -SAMUtils.compareMapqs(rec1.getMappingQuality(), rec2.getMappingQuality());
}
}
}