From fecba2cae5a3f61563fbcfa72f42e077a0d5aee4 Mon Sep 17 00:00:00 2001 From: kiran Date: Tue, 9 Jun 2009 03:21:14 +0000 Subject: [PATCH] Disabled option to show secondary quals as the definition has changed to conform to the spec and thus this printout is non-sensical. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@950 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/walkers/PileupWalker.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index 91c976d48..8b025bd93 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -32,8 +32,8 @@ public class PileupWalker extends LocusWalker implements TreeR @Argument(fullName="alwaysShowSecondBase",doc="If true, prints dummy bases for the second bases in the BAM file where they are missing",required=false) public boolean alwaysShowSecondBase = false; - @Argument(fullName="showSecondBaseQuals",doc="If true, prints out second base qualities in the pileup",required=false) - public boolean showSecondBaseQuals = false; + //@Argument(fullName="showSecondBaseQuals",doc="If true, prints out second base qualities in the pileup",required=false) + //public boolean showSecondBaseQuals = false; @Argument(fullName="qualsAsInts",doc="If true, prints out qualities in the pileup as comma-separated integers",required=false) public boolean qualsAsInts = false; @@ -62,12 +62,14 @@ public class PileupWalker extends LocusWalker implements TreeR } if ( secondBasePileup != null ) extras.append(" ").append(secondBasePileup); + /* if ( showSecondBaseQuals ) { String secondQualPileup = pileup.getSecondaryQualPileup(); if ( secondQualPileup == null ) secondQualPileup = Utils.dupString((char)(33), bases.length()); extras.append(" ").append(secondQualPileup); } + */ String rodString = ""; for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {