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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
This commit is contained in:
kiran 2009-06-09 03:21:14 +00:00
parent 5fa3f7ed3a
commit fecba2cae5
1 changed files with 4 additions and 2 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -32,8 +32,8 @@ public class PileupWalker extends LocusWalker<Integer, Integer> 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) @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; public boolean alwaysShowSecondBase = false;
@Argument(fullName="showSecondBaseQuals",doc="If true, prints out second base qualities in the pileup",required=false) //@Argument(fullName="showSecondBaseQuals",doc="If true, prints out second base qualities in the pileup",required=false)
public boolean showSecondBaseQuals = false; //public boolean showSecondBaseQuals = false;
@Argument(fullName="qualsAsInts",doc="If true, prints out qualities in the pileup as comma-separated integers",required=false) @Argument(fullName="qualsAsInts",doc="If true, prints out qualities in the pileup as comma-separated integers",required=false)
public boolean qualsAsInts = false; public boolean qualsAsInts = false;
@ -62,12 +62,14 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
} }
if ( secondBasePileup != null ) extras.append(" ").append(secondBasePileup); if ( secondBasePileup != null ) extras.append(" ").append(secondBasePileup);
/*
if ( showSecondBaseQuals ) { if ( showSecondBaseQuals ) {
String secondQualPileup = pileup.getSecondaryQualPileup(); String secondQualPileup = pileup.getSecondaryQualPileup();
if ( secondQualPileup == null ) if ( secondQualPileup == null )
secondQualPileup = Utils.dupString((char)(33), bases.length()); secondQualPileup = Utils.dupString((char)(33), bases.length());
extras.append(" ").append(secondQualPileup); extras.append(" ").append(secondQualPileup);
} }
*/
String rodString = ""; String rodString = "";
for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) { for ( ReferenceOrderedDatum datum : tracker.getAllRods() ) {