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One minor addition: to incorporate Pooled calling (and to be as general as possible), we allow the genotype calculation model to use rods if it wants. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1741 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-29 17:05:59 +00:00
parent 19bfe43173
commit 9ef80e3c3c
4 changed files with 8 additions and 4 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper; package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.genotype.GenotypeWriter; import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
import java.util.*; import java.util.*;
@ -82,7 +83,8 @@ public abstract class GenotypeCalculationModel implements Cloneable {
* *
* @return true if valid locus * @return true if valid locus
*/ */
public abstract boolean calculateGenotype(char ref, public abstract boolean calculateGenotype(RefMetaDataTracker tracker,
char ref,
AlignmentContext context, AlignmentContext context,
DiploidGenotypePriors priors); DiploidGenotypePriors priors);
} }

3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/MultiSampleAllMAFsGenotypeCalculationModel.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.genotype.GenotypeWriter; import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import java.util.Set; import java.util.Set;
@ -28,7 +29,7 @@ public class MultiSampleAllMAFsGenotypeCalculationModel extends GenotypeCalculat
return super.clone(); return super.clone();
} }
public boolean calculateGenotype(char ref, AlignmentContext context, DiploidGenotypePriors priors) { public boolean calculateGenotype(RefMetaDataTracker tracker, char ref, AlignmentContext context, DiploidGenotypePriors priors) {
// This is just a stub... // This is just a stub...
// TODO --- implement me // TODO --- implement me

3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotypeCalculationModel.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.genotyper; package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.GenotypeWriter; import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
@ -37,7 +38,7 @@ public class SingleSampleGenotypeCalculationModel extends GenotypeCalculationMod
return super.clone(); return super.clone();
} }
public boolean calculateGenotype(char ref, AlignmentContext context, DiploidGenotypePriors priors) { public boolean calculateGenotype(RefMetaDataTracker tracker, char ref, AlignmentContext context, DiploidGenotypePriors priors) {
GenotypeLikelihoods gl = GenotypeLikelihoodsFactory.makeGenotypeLikelihoods(baseModel, priors, defaultPlatform); GenotypeLikelihoods gl = GenotypeLikelihoodsFactory.makeGenotypeLikelihoods(baseModel, priors, defaultPlatform);
gl.setVerbose(VERBOSE); gl.setVerbose(VERBOSE);

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -90,7 +90,7 @@ public class UnifiedGenotyper extends LocusWalker<Integer, Integer> {
return 0; return 0;
DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, UAC.heterozygosity, DiploidGenotypePriors.PROB_OF_TRISTATE_GENOTYPE); DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, UAC.heterozygosity, DiploidGenotypePriors.PROB_OF_TRISTATE_GENOTYPE);
return ( gcm.calculateGenotype(ref, context, priors) ? 1 : 0 ); return ( gcm.calculateGenotype(tracker, ref, context, priors) ? 1 : 0 );
} }
/** /**