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Haiku: 

Eric is a fool.
Matt found his really dumb bug.
Eric is humbled.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2830 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-02-12 04:51:56 +00:00
parent d4e4120ca1
commit c6f6948f9d
1 changed files with 5 additions and 8 deletions
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13
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -291,14 +291,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
if ( writers != null ) {
for ( SAMFileWriter writer : writers.values() ) {
// TODO -- figure out why we're getting an exception thrown here
// TODO -- because we need to call close() to flush out the remaining reads from the writer
try {
writer.close();
if ( !SORT_ON_DISK )
((SortingSAMFileWriter)writer).getBaseWriter().close();
} catch (RuntimeException e) {}
HashSet<SAMFileWriter> uniqueWriters = new HashSet<SAMFileWriter>(writers.values());
for ( SAMFileWriter writer : uniqueWriters ) {
writer.close();
if ( !SORT_ON_DISK )
((SortingSAMFileWriter)writer).getBaseWriter().close();
}
}