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Adding --doNotWriteOriginalQuals argument to BQ recalibrator 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5286 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-02-22 04:00:00 +00:00
parent dee130ad1b
commit d7f98ccd9c
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -97,6 +97,8 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
private int SMOOTHING = 1;
@Argument(fullName="max_quality_score", shortName="maxQ", required = false, doc="The integer value at which to cap the quality scores, default=50")
private int MAX_QUALITY_SCORE = 50;
@Argument(fullName="doNotWriteOriginalQuals", shortName="noOQs", required=false, doc="If true, we will not write the original quality (OQ) tag for each read")
private boolean DO_NOT_WRITE_OQ = false;
/////////////////////////////
// Debugging-only Arguments
@ -378,7 +380,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
preserveQScores( originalQuals, recalQuals ); // Overwrite the work done if original quality score is too low
read.setBaseQualities( recalQuals ); // Overwrite old qualities with new recalibrated qualities
if ( read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG) == null ) { // Save the old qualities if the tag isn't already taken in the read
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));
}