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Fixed order-of-operations bug. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@919 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-06 03:22:56 +00:00
parent 819862e04e
commit ac5b7dd453
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java
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@ -117,7 +117,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
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)) {