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Improvement for the TGEN folks: when running in the solid recal mode of SET_Q_ZERO_BASE_N, update the NM tag if one was present in the read to reflect the new N's in the read. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4761 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-12-01 04:36:44 +00:00
parent a22b1b04e6
commit 0892daddb0
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -386,10 +386,14 @@ 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 && refBases != null && ! skipUQUpdate ) { if (! skipUQUpdate && refBases != null && read.getAttribute(SAMTag.UQ.name()) != 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));
} }
if (RAC.SOLID_RECAL_MODE == RecalDataManager.SOLID_RECAL_MODE.SET_Q_ZERO_BASE_N && refBases != null && read.getAttribute(SAMTag.NM.name()) != null) {
read.setAttribute(SAMTag.NM.name(), SequenceUtil.calculateSamNmTag(read, refBases.getBases(), read.getAlignmentStart() - 1, false));
}
return read; return read;
} }