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Re-allowing blacklist by read group id. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3571 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-06-16 19:45:44 +00:00
parent f003703912
commit c671864228
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
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@ -58,7 +58,11 @@ public class ReadGroupBlackListFilter implements SamRecordFilter {
SAMReadGroupRecord samReadGroupRecord = samRecord.getReadGroup(); SAMReadGroupRecord samReadGroupRecord = samRecord.getReadGroup();
if (samReadGroupRecord != null) { if (samReadGroupRecord != null) {
Object attribute = samReadGroupRecord.getAttribute(attributeType); Object attribute;
if ("ID".equals(attributeType) || "RG".equals(attributeType))
attribute = samReadGroupRecord.getId();
else
attribute = samReadGroupRecord.getAttribute(attributeType);
if (attribute != null && filterEntry.getValue().contains(attribute)) if (attribute != null && filterEntry.getValue().contains(attribute))
return true; return true;
} }