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Added the -maxQ argument to the list of arguments in the PG tag 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2627 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2010-01-19 15:55:23 +00:00
parent d61cafd19f
commit bca436578f
1 changed files with 1 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -240,6 +240,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
} }
} }
commandLineString += "pQ=" + PRESERVE_QSCORES_LESS_THAN + ", "; commandLineString += "pQ=" + PRESERVE_QSCORES_LESS_THAN + ", ";
commandLineString += "maxQ=" + MAX_QUALITY_SCORE + ", ";
commandLineString += "smoothing=" + SMOOTHING; commandLineString += "smoothing=" + SMOOTHING;
programRecord.setCommandLine( commandLineString ); programRecord.setCommandLine( commandLineString );
header.addProgramRecord( programRecord ); header.addProgramRecord( programRecord );