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Read groups are now sorted in the output data, for convenience 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1129 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-06-30 16:50:44 +00:00
parent fe421e5712
commit 9fca79ed62
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -205,7 +205,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
printInfo(recalTableStream);
recalTableStream.println("rg,pos,Qrep,dn,nBases,nMismatches,Qemp");
for (String readGroup : covariateCounter.getReadGroups()) {
for (String readGroup : new TreeSet<String>(covariateCounter.getReadGroups()) ) {
for ( RecalData datum: RecalData.sort(covariateCounter.getRecalData(readGroup)) ) {
if ( datum.N > 0 )
recalTableStream.format("%s%n", datum.toCSVString(collapsePos));