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Change for Tim: invalidate the MD tag (temporarily) if it exists in a read that gets realigned 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4228 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-09-08 13:59:09 +00:00
parent 65edbced36
commit cd2bfb09ef
1 changed files with 3 additions and 0 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -592,6 +592,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
read.setAttribute("NM", SequenceUtil.calculateSamNmTag(read, reference, (int)leftmostIndex-1)); read.setAttribute("NM", SequenceUtil.calculateSamNmTag(read, reference, (int)leftmostIndex-1));
if ( read.getAttribute(SAMTag.UQ.name()) != null ) if ( read.getAttribute(SAMTag.UQ.name()) != null )
read.setAttribute("UQ", SequenceUtil.sumQualitiesOfMismatches(read, reference, (int)leftmostIndex-1)); read.setAttribute("UQ", SequenceUtil.sumQualitiesOfMismatches(read, reference, (int)leftmostIndex-1));
// TODO -- this is only temporary until Tim adds code to recalculate this value
if ( read.getAttribute(SAMTag.MD.name()) != null )
read.setAttribute("MD", null);
} }
} }
} }