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Filter,merge performs much better than merge,filter. Many thanks to Eric for checking in an integration test that so compellingly demonstrates this. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3011 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2010-03-16 16:23:37 +00:00
parent 6dd5f192e7
commit 59045ccb28
1 changed files with 5 additions and 5 deletions
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10
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
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@ -264,16 +264,16 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
Map<SAMFileReader,CloseableIterator<SAMRecord>> readerToIteratorMap = new HashMap<SAMFileReader,CloseableIterator<SAMRecord>>(); Map<SAMFileReader,CloseableIterator<SAMRecord>> readerToIteratorMap = new HashMap<SAMFileReader,CloseableIterator<SAMRecord>>();
for(SAMReaderID id: getReaderIDs()) { for(SAMReaderID id: getReaderIDs()) {
SAMFileReader2 reader2 = (SAMFileReader2)readers.getReader(id); SAMFileReader2 reader2 = (SAMFileReader2)readers.getReader(id);
List<Chunk> chunks = shard.getChunks().get(id); CloseableIterator<SAMRecord> iterator = reader2.iterator(shard.getChunks().get(id));
readerToIteratorMap.put(reader2,reader2.iterator(chunks)); if(shard.getFilter() != null)
iterator = new FilteringIterator(iterator,shard.getFilter());
readerToIteratorMap.put(reader2,iterator);
} }
SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers.values(),SAMFileHeader.SortOrder.coordinate,true); SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers.values(),SAMFileHeader.SortOrder.coordinate,true);
// Set up merging and filtering to dynamically merge together multiple BAMs and filter out records not in the shard set. // Set up merging to dynamically merge together multiple BAMs.
CloseableIterator<SAMRecord> iterator = new MergingSamRecordIterator(headerMerger,readerToIteratorMap,true); CloseableIterator<SAMRecord> iterator = new MergingSamRecordIterator(headerMerger,readerToIteratorMap,true);
if(shard.getFilter() != null)
iterator = new FilteringIterator(iterator,shard.getFilter());
return applyDecoratingIterators(enableVerification, return applyDecoratingIterators(enableVerification,
new ReleasingIterator(readers,StingSAMIteratorAdapter.adapt(reads,iterator)), new ReleasingIterator(readers,StingSAMIteratorAdapter.adapt(reads,iterator)),