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

Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Guillermo del Angel 2012-05-08 10:42:12 -04:00
parent 7584b1ea17 5cf4fd63c2
commit 33a1dd2048
1 changed files with 5 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
View File

@ -425,7 +425,11 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
read.setBaseQualities(recalQuals); // Overwrite old qualities with new recalibrated qualities
if (!DO_NOT_WRITE_OQ && read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG) == null) { // Save the old qualities if the tag isn't already taken in the read
read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, SAMUtils.phredToFastq(originalQuals));
try {
read.setAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG, SAMUtils.phredToFastq(originalQuals));
} catch (IllegalArgumentException e) {
throw new UserException.MalformedBAM(read, "illegal base quality encountered; " + e.getMessage());
}
}
if (!skipUQUpdate && refBases != null && read.getAttribute(SAMTag.UQ.name()) != null) {