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Yikes! VariantEval was always loading genotypes unnecessarily when no sample list was provided because the order of the checks in the if statement wasn't optimal. This results in a massive performance penalty when running with many-sample VCFs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4570 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-25 20:30:23 +00:00
parent 0d97394c4f
commit 67a776d53c
1 changed files with 1 additions and 2 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.apache.log4j.Logger;
import org.broad.tribble.util.variantcontext.MutableVariantContext;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.StandardVCFWriter;
import org.broad.tribble.vcf.VCFConstants;
import org.broad.tribble.vcf.VCFWriter;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -672,7 +671,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
VariantContext vc = contexts.size() == 1 ? contexts.iterator().next() : null;
if ( vc != null && vc.hasGenotypes(SAMPLES_LIST) && SAMPLES_LIST.size() > 0 ) {
if ( vc != null && SAMPLES_LIST.size() > 0 && vc.hasGenotypes(SAMPLES_LIST) ) {
//if ( ! name.equals("eval") ) logger.info(String.format("subsetting VC %s", vc));
vc = vc.subContextFromGenotypes(vc.getGenotypes(SAMPLES_LIST).values());
HashMap<String,Object> newAts = new HashMap<String,Object>(vc.getAttributes());