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Fixed edge case bug in cleaner: when no -L argument is used and a target interval abuts the end of the reference genome, we'll NullPointer at the first unmapped read. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3293 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-05-04 16:49:21 +00:00
parent 510b3efcc2
commit 03bea70f3a
1 changed files with 28 additions and 17 deletions
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45
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -289,10 +289,18 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
return 0;
}
// edge case: when the last target interval abuts the end of the genome, we'll get one of the
// unmapped reads while the currentInterval still isn't null. We need to trigger the cleaning
// at this point without trying to create a GenomeLoc.
if ( read.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX ) {
cleanAndCallMap(ref, read, metaDataTracker, null);
return 0;
}
GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read);
// hack to get around unmapped reads having screwy locations
if ( readLoc.getStop() == 0 )
readLoc = GenomeLocParser.createGenomeLoc(readLoc.getContig(), readLoc.getStart(), readLoc.getStart());
readLoc = GenomeLocParser.createGenomeLoc(readLoc.getContigIndex(), readLoc.getStart(), readLoc.getStart());
if ( readLoc.isBefore(currentInterval) || ReadUtils.is454Read(read) ) {
// TODO -- it would be nice if we could use indels from 454 reads as alternate consenses
@ -321,27 +329,30 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
}
else { // the read is past the current interval
clean(readsToClean);
knownIndelsToTry.clear();
// merge the two sets for emission
readsNotToClean.addAll(readsToClean.getReads());
emit(readsNotToClean);
readsToClean.clear();
readsNotToClean.clear();
do {
currentInterval = intervals.hasNext() ? intervals.next() : null;
} while ( currentInterval != null && currentInterval.isBefore(readLoc) );
// call back into map now that the state has been updated
map(ref, read,metaDataTracker);
cleanAndCallMap(ref, read, metaDataTracker, readLoc);
}
return 0;
}
private void cleanAndCallMap(char[] ref, SAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {
clean(readsToClean);
knownIndelsToTry.clear();
// merge the two sets for emission
readsNotToClean.addAll(readsToClean.getReads());
emit(readsNotToClean);
readsToClean.clear();
readsNotToClean.clear();
do {
currentInterval = intervals.hasNext() ? intervals.next() : null;
} while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) );
// call back into map now that the state has been updated
map(ref, read, metaDataTracker);
}
public Integer reduceInit() {
return 0;
}