From 59045ccb28b5e83bd846fb983ea240d9549a6087 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 16 Mar 2010 16:23:37 +0000
Subject: [PATCH] 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
---
 .../simpleDataSources/BlockDrivenSAMDataSource.java    | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
index 53b9061b3..b575ef6b8 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
@@ -264,16 +264,16 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
         Map<SAMFileReader,CloseableIterator<SAMRecord>> readerToIteratorMap = new HashMap<SAMFileReader,CloseableIterator<SAMRecord>>();
         for(SAMReaderID id: getReaderIDs()) {
             SAMFileReader2 reader2 = (SAMFileReader2)readers.getReader(id);
-            List<Chunk> chunks = shard.getChunks().get(id);
-            readerToIteratorMap.put(reader2,reader2.iterator(chunks));
+            CloseableIterator<SAMRecord> iterator = reader2.iterator(shard.getChunks().get(id));
+            if(shard.getFilter() != null)
+                iterator = new FilteringIterator(iterator,shard.getFilter());
+            readerToIteratorMap.put(reader2,iterator);
         }
 
         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);
-        if(shard.getFilter() != null)
-            iterator = new FilteringIterator(iterator,shard.getFilter());
 
         return applyDecoratingIterators(enableVerification,
                 new ReleasingIterator(readers,StingSAMIteratorAdapter.adapt(reads,iterator)),