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temporary patch until Picard (hopefully) fixes the NM calculation to deal with reads that align off the end of the contig 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5630 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-13 19:18:18 +00:00
parent fa6468d167
commit 91d308fc6d
1 changed files with 12 additions and 7 deletions
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19
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -769,9 +769,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
SAMRecord read = aRead.getRead();
read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));
// before we fix the attribute tags we first need make sure we have enough of the reference sequence
int neededBasesToLeft = Math.max(leftmostIndex - read.getAlignmentStart(), 0);
int neededBasesToRight = Math.max(read.getAlignmentEnd() - leftmostIndex - reference.length + 1, 0);
// before we fix the attribute tags we first need to make sure we have enough of the reference sequence
int neededBasesToLeft = leftmostIndex - read.getAlignmentStart();
int neededBasesToRight = read.getAlignmentEnd() - leftmostIndex - reference.length + 1;
int neededBases = Math.max(neededBasesToLeft, neededBasesToRight);
if ( neededBases > 0 ) {
int padLeft = Math.max(leftmostIndex-neededBases, 1);
@ -781,10 +781,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
// now, fix the attribute tags
if ( read.getAttribute(SAMTag.NM.name()) != null )
read.setAttribute(SAMTag.NM.name(), SequenceUtil.calculateSamNmTag(read, reference, leftmostIndex-1));
if ( read.getAttribute(SAMTag.UQ.name()) != null )
read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, reference, leftmostIndex-1));
// TODO -- get rid of this try block when Picard does the right thing for reads aligned off the end of the reference
try {
if ( read.getAttribute(SAMTag.NM.name()) != null )
read.setAttribute(SAMTag.NM.name(), SequenceUtil.calculateSamNmTag(read, reference, leftmostIndex-1));
if ( read.getAttribute(SAMTag.UQ.name()) != null )
read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, reference, leftmostIndex-1));
} catch (Exception e) {
// ignore it
}
// TODO -- this is only temporary until Tim adds code to recalculate this value
if ( read.getAttribute(SAMTag.MD.name()) != null )
read.setAttribute(SAMTag.MD.name(), null);