From 9da04fd9acfaa29157fc11646536c726d7a9688b Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 5 Jun 2009 03:14:17 +0000 Subject: [PATCH] Cleaned up error warning in case no PL groups are present. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@907 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/gatk/walkers/CovariateCounterWalker.java | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java index 4dad8e32c..745e40a2e 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java @@ -93,6 +93,8 @@ public class CovariateCounterWalker extends LocusWalker { public void initialize() { for (SAMReadGroupRecord readGroup : this.getToolkit().getEngine().getSAMHeader().getReadGroups()) { + if( readGroup.getAttribute("PL") == null ) + Utils.warnUser(String.format("PL attribute for read group %s is unset; assuming all reads are illumina",readGroup.getReadGroupId())); data.put(readGroup.getReadGroupId(), new RecalData[MAX_READ_LENGTH+1][MAX_QUAL_SCORE+1][NDINUCS]); for ( int i = 0; i < MAX_READ_LENGTH+1; i++) { for ( int j = 0; j < MAX_QUAL_SCORE+1; j++) { @@ -108,12 +110,6 @@ public class CovariateCounterWalker extends LocusWalker { } public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { - // No PL attribute? Warn the user and keep going. - for(SAMReadGroupRecord readGroup: getToolkit().getEngine().getSAMHeader().getReadGroups()) { - if( readGroup.getAttribute("PL") == null ) - Utils.warnUser(String.format("PL attribute for read group %s is unset; assuming all reads are illumina",readGroup.getReadGroupId())); - } - rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null); if ( dbsnp == null || !dbsnp.isSNP() ) { List reads = context.getReads();