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'Okay, now I'm absolutely certain that there are no more bugs in the constrained writer.' 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5353 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-03-02 03:48:40 +00:00
parent 880c607d79
commit 660998065b
1 changed files with 21 additions and 10 deletions
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31
java/src/org/broadinstitute/sting/utils/sam/ConstrainedMateFixingSAMFileWriter.java
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@ -185,18 +185,29 @@ public class ConstrainedMateFixingSAMFileWriter implements SAMFileWriter {
if ( newRead.getReadPairedFlag() ) {
SAMRecord mate = forMateMatching.get(newRead.getReadName());
if ( mate != null ) {
boolean reQueueMate = mate.getReadUnmappedFlag() && ! newRead.getReadUnmappedFlag();
if ( reQueueMate ) {
// the mate was unmapped, but newRead was mapped, so the mate may have been moved
// to be next-to newRead, so needs to be reinserted into the waitingReads queue
// note -- this must be called before the setMateInfo call below
if ( ! waitingReads.remove(mate) )
throw new ReviewedStingException("BUG: removal of mate failed at " + mate);
// Frustratingly, Picard's setMateInfo() method unaligns (by setting the reference contig
// to '*') read pairs when both of their flags have the unmapped bit set. This is problematic
// when trying to emit reads in coordinate order because all of a sudden we have reads in the
// middle of the bam file that now belong at the end - and any mapped reads that get emitted
// after them trigger an exception in the writer. For our purposes, because we shouldn't be
// moving read pairs when they are both unmapped anyways, we'll just not run fix mates on them.
boolean doNotFixMates = newRead.getReadUnmappedFlag() && mate.getReadUnmappedFlag();
if ( !doNotFixMates ) {
boolean reQueueMate = mate.getReadUnmappedFlag() && ! newRead.getReadUnmappedFlag();
if ( reQueueMate ) {
// the mate was unmapped, but newRead was mapped, so the mate may have been moved
// to be next-to newRead, so needs to be reinserted into the waitingReads queue
// note -- this must be called before the setMateInfo call below
if ( ! waitingReads.remove(mate) )
throw new ReviewedStingException("BUG: removal of mate failed at " + mate);
}
// we've already seen our mate -- set the mate info and remove it from the map
SamPairUtil.setMateInfo(mate, newRead, null);
if ( reQueueMate ) waitingReads.add(mate);
}
// we've already seen our mate -- set the mate info and remove it from the map
SamPairUtil.setMateInfo(mate, newRead, null);
if ( reQueueMate ) waitingReads.add(mate);
forMateMatching.remove(newRead.getReadName());
} else {
forMateMatching.put(newRead.getReadName(), newRead);