From f552aede420a62173784d19a5cfd4a13b77d17cc Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 4 Oct 2011 06:50:12 -0700
Subject: [PATCH] Only provide the sample names in the BAM file for efficiency

---
 .../sting/gatk/executive/LinearMicroScheduler.java             | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
index a5d1370ba..deafcd0cc 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
@@ -13,6 +13,7 @@ import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.utils.SampleUtils;
 
 import java.util.Collection;
 
@@ -57,7 +58,7 @@ public class LinearMicroScheduler extends MicroScheduler {
             if(shard.getShardType() == Shard.ShardType.LOCUS) {
                 LocusWalker lWalker = (LocusWalker)walker;
                 WindowMaker windowMaker = new WindowMaker(shard, engine.getGenomeLocParser(),
-                        getReadIterator(shard), shard.getGenomeLocs(), engine.getSampleDB().getSampleNames());
+                        getReadIterator(shard), shard.getGenomeLocs(), SampleUtils.getSAMFileSamples(engine));
                 for(WindowMaker.WindowMakerIterator iterator: windowMaker) {
                     ShardDataProvider dataProvider = new LocusShardDataProvider(shard,iterator.getSourceInfo(),engine.getGenomeLocParser(),iterator.getLocus(),iterator,reference,rods);
                     Object result = traversalEngine.traverse(walker, dataProvider, accumulator.getReduceInit());