zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
View File

@ -115,8 +115,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
private boolean isSupportedReadGroup( SAMReadGroupRecord readGroup ) { private boolean isSupportedReadGroup( SAMReadGroupRecord readGroup ) {
for( String platform: platforms ) { for( String platform: platforms ) {
platform = platform.trim(); platform = platform.trim();
if( readGroup.getAttribute("PL") == null || if( platform.equals("*") ||
platform.equals("*") || readGroup.getAttribute("PL") == null ||
readGroup.getAttribute("PL").toString().equalsIgnoreCase(platform) ) readGroup.getAttribute("PL").toString().equalsIgnoreCase(platform) )
return true; return true;
} }
@ -208,7 +208,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
for (String readGroup : new TreeSet<String>(covariateCounter.getReadGroups()) ) { for (String readGroup : new TreeSet<String>(covariateCounter.getReadGroups()) ) {
for ( RecalData datum: RecalData.sort(covariateCounter.getRecalData(readGroup)) ) { for ( RecalData datum: RecalData.sort(covariateCounter.getRecalData(readGroup)) ) {
if ( datum.N > 0 ) if ( datum.N > 0 )
recalTableStream.format("%s%n", datum.toCSVString(collapsePos)); recalTableStream.println(datum.toCSVString(collapsePos));
} }
} }
} }