diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java index 8bf7ef47a..a2b41b6a2 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java @@ -115,8 +115,8 @@ public class CovariateCounterWalker extends LocusWalker { 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 { for (String readGroup : new TreeSet(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)); } } }