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Do not die in --cycleOnly mode when the lane is not paired end, just count all single end basequals into the first column and leave the second column filled with 0s 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2778 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-02-04 19:48:12 +00:00
parent a3cd56897d
commit 152f65b362
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
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@ -82,7 +82,11 @@ public class QualityScoreByStrandWalker extends LocusWalker<StrandedCounts,Stran
if ( ! useCycle ) { if ( ! useCycle ) {
counts.updateLocus( (int) e.getQual(), ! e.getRead().getReadNegativeStrandFlag() ); counts.updateLocus( (int) e.getQual(), ! e.getRead().getReadNegativeStrandFlag() );
} else { } else {
counts.updateLocus( (int) e.getQual(), ! e.getRead().getFirstOfPairFlag() ); if ( e.getRead().getReadPairedFlag() ) {
counts.updateLocus( (int) e.getQual(), e.getRead().getFirstOfPairFlag() );
} else {
counts.updateLocus( (int) e.getQual(), true );
}
} }
} }