From ac5b7dd4533307970805589ef65944d60717bab6 Mon Sep 17 00:00:00 2001 From: hanna Date: Sat, 6 Jun 2009 03:22:56 +0000 Subject: [PATCH] Fixed order-of-operations bug. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@919 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/playground/gatk/walkers/CovariateCounterWalker.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 745e40a2e..fd7c4e666 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java @@ -117,7 +117,7 @@ public class CovariateCounterWalker extends LocusWalker { for (int i =0; i < reads.size(); i++ ) { SAMRecord read = reads.get(i); SAMReadGroupRecord readGroup = read.getHeader().getReadGroup((String)read.getAttribute("RG")); - if ( readGroup.getAttribute("PL") == null || "ILLUMINA".equalsIgnoreCase(readGroup.getAttribute("PL").toString()) && + if ( (readGroup.getAttribute("PL") == null || "ILLUMINA".equalsIgnoreCase(readGroup.getAttribute("PL").toString())) && !read.getReadNegativeStrandFlag() && (READ_GROUP.equals("none") || read.getAttribute("RG") != null && read.getAttribute("RG").equals(READ_GROUP)) && (read.getMappingQuality() >= MIN_MAPPING_QUALITY)) {