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ExperimentalReadShardBalancer: close() exhausted iterators 

Fixes a truly awful SAMReaders resource leak reported by Eric -- thanks Eric!
This commit is contained in:
David Roazen 2012-09-24 14:45:53 -04:00
parent 9fd30d6f1c
commit 0b488cce66
1 changed files with 4 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ExperimentalReadShardBalancer.java
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@ -89,6 +89,10 @@ public class ExperimentalReadShardBalancer extends ShardBalancer {
// If we've exhausted the current file pointer of reads, move to the next file pointer (if there is one): // If we've exhausted the current file pointer of reads, move to the next file pointer (if there is one):
if ( currentFilePointerReadsIterator != null && ! currentFilePointerReadsIterator.hasNext() ) { if ( currentFilePointerReadsIterator != null && ! currentFilePointerReadsIterator.hasNext() ) {
// Close the old, exhausted chain of iterators to release resources
currentFilePointerReadsIterator.close();
do { do {
advanceFilePointer(); advanceFilePointer();
} while ( currentFilePointer != null && isEmpty(currentFilePointer.fileSpans) ); // skip empty file pointers } while ( currentFilePointer != null && isEmpty(currentFilePointer.fileSpans) ); // skip empty file pointers