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Bug fixes for edge cases and filtration in the earlier performance fixes. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2989 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-12 04:46:08 +00:00
parent 1e170369b9
commit 7aa7a5f9b8
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java
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@ -115,16 +115,17 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
} }
if(selectedReaders.size() > 0) { if(selectedReaders.size() > 0) {
filter = new ReadOverlapFilter(currentFilePointer.locations);
BAMFormatAwareShard shard = new BlockDelimitedReadShard(dataSource.getReadsInfo(),selectedReaders,filter,Shard.ShardType.READ); BAMFormatAwareShard shard = new BlockDelimitedReadShard(dataSource.getReadsInfo(),selectedReaders,filter,Shard.ShardType.READ);
dataSource.fillShard(shard); dataSource.fillShard(shard);
if(!shard.isBufferEmpty()) { if(!shard.isBufferEmpty()) {
filter = new ReadOverlapFilter(currentFilePointer.locations);
nextShard = shard; nextShard = shard;
break; break;
} }
} }
selectedReaders.clear();
currentFilePointer = filePointerIterator.hasNext() ? filePointerIterator.next() : null; currentFilePointer = filePointerIterator.hasNext() ? filePointerIterator.next() : null;
} }
} }