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Tiny bug fix 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4793 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-12-05 18:48:33 +00:00
parent 44feb4a362
commit 80f32712dc
1 changed files with 3 additions and 2 deletions
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5
java/src/org/broadinstitute/sting/utils/BAQ.java
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@ -421,7 +421,7 @@ public class BAQ {
public BAQCalculationResult calcBAQFromHMM(SAMRecord read, IndexedFastaSequenceFile refReader) {
// start is alignment start - band width / 2 - size of first I element, if there is one. Stop is similar
int offset = getBandWidth() / 2;
long start = read.getAlignmentStart() - offset - getFirstInsertionOffset(read);
long start = Math.max(read.getAlignmentStart() - offset - getFirstInsertionOffset(read), 0);
long stop = read.getAlignmentEnd() + offset + getLastInsertionOffset(read);
if ( stop > refReader.getSequenceDictionary().getSequence(read.getReferenceName()).getSequenceLength() ) {
@ -431,7 +431,8 @@ public class BAQ {
// now that we have the start and stop, get the reference sequence covering it
ReferenceSequence refSeq = refReader.getSubsequenceAt(read.getReferenceName(), start, stop);
return calcBAQFromHMM(read, refSeq.getBases(), - (offset + getFirstInsertionOffset(read)));
// todo -- think about last tiny bit of logic -- should be fine but need to convince myself that it's 100% correct
return calcBAQFromHMM(read, refSeq.getBases(), (int)(start - read.getAlignmentStart()));
}
}