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Merge pull request #316 from broadinstitute/md_filter_counting 

Bugfix for counting of applied filters
This commit is contained in:
Valentin Ruano Rubio 2013-07-08 10:58:47 -07:00
parent 380a01ddc0 9df58314ab
commit ac77a4c699
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java
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@ -115,10 +115,10 @@ public class CountingFilteringIterator implements CloseableIterator<SAMRecord> {
public void close() { public void close() {
CloserUtil.close(iterator); CloserUtil.close(iterator);
for ( final CountingReadFilter filter : filters )
privateRuntimeMetrics.setFilterCount(filter.readFilter.getClass().getSimpleName(), filter.counter);
// update the global metrics with all the data we collected here // update the global metrics with all the data we collected here
globalRuntimeMetrics.incrementMetrics(privateRuntimeMetrics); globalRuntimeMetrics.incrementMetrics(privateRuntimeMetrics);
for ( final CountingReadFilter filter : filters )
globalRuntimeMetrics.setFilterCount(filter.readFilter.getClass().getSimpleName(), filter.counter);
} }
/** /**