zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Bug fix for damoskow in TableRecalibration. Shouldn't try to update the reference mismatch rate tag for an unmapped read. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4028 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-08-13 18:57:07 +00:00
parent 80a70ccf03
commit 222f61df87
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
View File

@ -375,7 +375,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, SAMUtils.phredToFastq(originalQuals)); read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, SAMUtils.phredToFastq(originalQuals));
} }
if (read.getAttribute(SAMTag.UQ.name()) != null) { if (read.getAttribute(SAMTag.UQ.name()) != null && refBases != null) {
read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, refBases.getBases(), read.getAlignmentStart() - 1, false)); read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, refBases.getBases(), read.getAlignmentStart() - 1, false));
} }