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Only provide the sample names in the BAM file for efficiency

This commit is contained in:
Mark DePristo 2011-10-04 06:50:12 -07:00
parent a27641e1fc
commit f552aede42
1 changed files with 2 additions and 1 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
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@ -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());