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Fixed read group blacklist filter to look only at readgroups (and not the read's themselves). Otherwise, it fails when attribute tags with different meanings show up in both places (e.g. SM). Added performance improvement. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3567 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-16 19:14:37 +00:00
parent e77f76f8e1
commit d7f3102c3f
1 changed files with 7 additions and 17 deletions
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24
java/src/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java
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@ -37,13 +37,9 @@ import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.text.XReadLines;
/**
* Removes records matching the read group tag and match string.
* For example each of the filter values:
* Removes records matching the read group tag and exact match string.
* For example, this filter value:
* PU:1000G-mpimg-080821-1_1
* PU:1000G-mpimg-080821
* PU:mpimg-080821-1_1
* PU:mpimg-080821
*
* would filter out a read with the read group PU:1000G-mpimg-080821-1_1
*/
public class ReadGroupBlackListFilter implements SamRecordFilter {
@ -60,18 +56,12 @@ public class ReadGroupBlackListFilter implements SamRecordFilter {
for (Entry<String, Collection<String>> filterEntry : filterEntries) {
String attributeType = filterEntry.getKey();
Object attribute = samRecord.getAttribute(attributeType);
if (attribute == null) {
SAMReadGroupRecord samReadGroupRecord = samRecord.getReadGroup();
if (samReadGroupRecord != null) {
attribute = samReadGroupRecord.getAttribute(attributeType);
}
SAMReadGroupRecord samReadGroupRecord = samRecord.getReadGroup();
if (samReadGroupRecord != null) {
Object attribute = samReadGroupRecord.getAttribute(attributeType);
if (attribute != null && filterEntry.getValue().contains(attribute))
return true;
}
if (attribute != null)
for (String filterValue : filterEntry.getValue())
if (attribute.toString().contains(filterValue))
return true;
}
return false;