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Cleanup. INDELS model is now disconnected (and renamed 'DINDEL' in preparation for adding plumbing for Guillermo soon) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4106 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-25 14:52:51 +00:00
parent 3dc78855fd
commit b4baa3eb8f
6 changed files with 11 additions and 21 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
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@ -71,7 +71,7 @@ public class BatchedCallsMerger extends LocusWalker<VariantContext, Integer> imp
public boolean includeReadsWithDeletionAtLoci() { return true; } public boolean includeReadsWithDeletionAtLoci() { return true; }
// enable extended events for indels // enable extended events for indels
public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS; } public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.DINDEL; }
public void initialize() { public void initialize() {

8
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
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@ -37,14 +37,8 @@ import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import java.util.*; import java.util.*;
public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalculationModel { public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalculationModel {
/**
* Should we enable the experimental genotype likelihood calculations?
*/
protected boolean useExptGenotypeLikelihoods = false;
protected DiploidGenotypeCalculationModel(boolean useExptGenotypeLikelihoods) { protected DiploidGenotypeCalculationModel() {}
this.useExptGenotypeLikelihoods = useExptGenotypeLikelihoods;
}
// the GenotypeLikelihoods map // the GenotypeLikelihoods map
private HashMap<String, GenotypeLikelihoods> GLs = new HashMap<String, GenotypeLikelihoods>(); private HashMap<String, GenotypeLikelihoods> GLs = new HashMap<String, GenotypeLikelihoods>();

3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
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@ -21,8 +21,7 @@ public abstract class GenotypeCalculationModel implements Cloneable {
public enum Model { public enum Model {
JOINT_ESTIMATE, JOINT_ESTIMATE,
JOINT_ESTIMATE_EXPT_GL, DINDEL
INDELS
} }
protected UnifiedArgumentCollection UAC; protected UnifiedArgumentCollection UAC;

13
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModelFactory.java
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@ -55,14 +55,13 @@ public class GenotypeCalculationModelFactory {
GenotypeCalculationModel gcm; GenotypeCalculationModel gcm;
switch ( UAC.genotypeModel ) { switch ( UAC.genotypeModel ) {
case JOINT_ESTIMATE: case JOINT_ESTIMATE:
case JOINT_ESTIMATE_EXPT_GL: gcm = new DiploidGenotypeCalculationModel();
boolean useExptGenotypeLikelihoods = UAC.genotypeModel == JOINT_ESTIMATE_EXPT_GL;
gcm = new DiploidGenotypeCalculationModel(useExptGenotypeLikelihoods);
break; break;
case INDELS: case DINDEL:
gcm = new SimpleIndelCalculationModel(); throw new UnsupportedOperationException("The Dindel-based genotype likelihoods model is not currently supported");
break; //gcm = new SimpleIndelCalculationModel();
default: throw new RuntimeException("Unexpected GenotypeCalculationModel " + UAC.genotypeModel); //break;
default: throw new IllegalArgumentException("Unexpected GenotypeCalculationModel " + UAC.genotypeModel);
} }
gcm.initialize(samples, logger, UAC, verboseWriter); gcm.initialize(samples, logger, UAC, verboseWriter);

4
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -37,8 +37,6 @@ import org.broadinstitute.sting.utils.vcf.VCFUtils;
import java.util.*; import java.util.*;
import java.io.PrintStream; import java.io.PrintStream;
import java.io.File;
import java.io.FileNotFoundException;
/** /**
@ -85,7 +83,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
public boolean includeReadsWithDeletionAtLoci() { return true; } public boolean includeReadsWithDeletionAtLoci() { return true; }
// enable extended events for indels // enable extended events for indels
public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.INDELS; } public boolean generateExtendedEvents() { return UAC.genotypeModel == GenotypeCalculationModel.Model.DINDEL; }
/** /**
* Inner class for collecting output statistics from the UG * Inner class for collecting output statistics from the UG

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -175,7 +175,7 @@ public class UnifiedGenotyperEngine {
return null; return null;
// are there too many deletions in the pileup? // are there too many deletions in the pileup?
if ( UAC.genotypeModel != GenotypeCalculationModel.Model.INDELS && if ( UAC.genotypeModel != GenotypeCalculationModel.Model.DINDEL &&
isValidDeletionFraction(UAC.MAX_DELETION_FRACTION) && isValidDeletionFraction(UAC.MAX_DELETION_FRACTION) &&
(double)pileup.getNumberOfDeletions() / (double)pileup.size() > UAC.MAX_DELETION_FRACTION ) (double)pileup.getNumberOfDeletions() / (double)pileup.size() > UAC.MAX_DELETION_FRACTION )
return null; return null;