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checkin for removal 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4237 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-09-09 02:32:46 +00:00
parent 5119bdb55e
commit 8708753a6a
1 changed files with 11 additions and 2 deletions
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13
java/src/org/broadinstitute/sting/playground/gatk/walkers/QSampleWalker.java
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@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.genotyper.BatchedCallsMerger;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
@ -110,7 +111,15 @@ public class QSampleWalker extends RodWalker<Integer, Integer> implements TreeRe
if ( genotypesVC == null ) if ( genotypesVC == null )
return 0; // protect ourselves for runs with BTI return 0; // protect ourselves for runs with BTI
VariantCallContext vcc = UG_engine.runGenotyper(tracker, ref, context); // set of het samples
Set<String> hetSamples = new HashSet<String>();
for ( String sample : samples ) {
if ( genotypesVC.getGenotype(sample).isHet() )
hetSamples.add(sample);
}
AlignmentContext hetsContext = BatchedCallsMerger.filterForSamples(context.getBasePileup(), hetSamples);
VariantCallContext vcc = UG_engine.runGenotyper(tracker, ref, hetsContext);
logger.info(String.format("Visiting site %s", context.getLocation())); logger.info(String.format("Visiting site %s", context.getLocation()));
for ( String sample : samples ) { for ( String sample : samples ) {
@ -135,7 +144,7 @@ public class QSampleWalker extends RodWalker<Integer, Integer> implements TreeRe
private static int HET_INDEX = 1; private static int HET_INDEX = 1;
private double scoreSample(String sample, VariantCallContext vcc) { private double scoreSample(String sample, VariantCallContext vcc) {
if ( vcc == null || vcc.vc == null || vcc.vc.getGenotype(sample) == null ) if ( vcc == null || vcc.vc == null || vcc.vc.getGenotype(sample) == null )
return 0.0; return 0.33;
else { else {
// get GLs // get GLs
GenotypeLikelihoods gl = vcc.vc.getGenotype(sample).getLikelihoods(); GenotypeLikelihoods gl = vcc.vc.getGenotype(sample).getLikelihoods();