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Simple performance improvements 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1166 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-07-03 16:45:23 +00:00
parent 0d00823332
commit bcda66d2db
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -115,8 +115,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
private boolean isSupportedReadGroup( SAMReadGroupRecord readGroup ) {
for( String platform: platforms ) {
platform = platform.trim();
if( readGroup.getAttribute("PL") == null ||
platform.equals("*") ||
if( platform.equals("*") ||
readGroup.getAttribute("PL") == null ||
readGroup.getAttribute("PL").toString().equalsIgnoreCase(platform) )
return true;
}
@ -208,7 +208,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
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));
recalTableStream.println(datum.toCSVString(collapsePos));
}
}
}