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Fixes for SLOD: 1) didn't work properly for multi-allelics (randomly chose an allele, possibly one that wasn't genotyped in the full context); 2) in cases when there were more alt alleles than the max allowed and the user is calculating SB, we would recompute the best alt alleles(s); 3) for some reason, we were recomputing the LOD for the full context when we'd already done that. Given that this passes integration tests on my end, this should be the last commit before the release.

This commit is contained in:
Eric Banks 2012-03-12 01:07:07 -04:00
parent 1ee46e5c06
commit b4749757f8
4 changed files with 34 additions and 34 deletions
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33
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
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@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.List;
import java.util.Map;
@ -76,24 +77,24 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
/**
* Can be overridden by concrete subclasses
*
* @param tracker rod data
* @param ref reference context
* @param contexts stratified alignment contexts
* @param contextType stratified context type
* @param priors priors to use for GLs
* @param alternateAlleleToUse the alternate allele to use, null if not set
* @param useBAQedPileup should we use the BAQed pileup or the raw one?
* @param locParser Genome Loc Parser
* @param tracker rod data
* @param ref reference context
* @param contexts stratified alignment contexts
* @param contextType stratified context type
* @param priors priors to use for GLs
* @param alternateAllelesToUse the alternate allele to use, null if not set
* @param useBAQedPileup should we use the BAQed pileup or the raw one?
* @param locParser Genome Loc Parser
* @return variant context where genotypes are no-called but with GLs
*/
public abstract VariantContext getLikelihoods(RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, AlignmentContext> contexts,
AlignmentContextUtils.ReadOrientation contextType,
GenotypePriors priors,
Allele alternateAlleleToUse,
boolean useBAQedPileup,
GenomeLocParser locParser);
public abstract VariantContext getLikelihoods(final RefMetaDataTracker tracker,
final ReferenceContext ref,
final Map<String, AlignmentContext> contexts,
final AlignmentContextUtils.ReadOrientation contextType,
final GenotypePriors priors,
final List<Allele> alternateAllelesToUse,
final boolean useBAQedPileup,
final GenomeLocParser locParser);
protected int getFilteredDepth(ReadBackedPileup pileup) {

15
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -284,13 +284,14 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
private final static EnumSet<VariantContext.Type> allowableTypes = EnumSet.of(VariantContext.Type.INDEL, VariantContext.Type.MIXED);
public VariantContext getLikelihoods(RefMetaDataTracker tracker,
ReferenceContext ref,
Map<String, AlignmentContext> contexts,
AlignmentContextUtils.ReadOrientation contextType,
GenotypePriors priors,
Allele alternateAlleleToUse,
boolean useBAQedPileup, GenomeLocParser locParser) {
public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
final ReferenceContext ref,
final Map<String, AlignmentContext> contexts,
final AlignmentContextUtils.ReadOrientation contextType,
final GenotypePriors priors,
final List<Allele> alternateAllelesToUse,
final boolean useBAQedPileup,
final GenomeLocParser locParser) {
if (tracker == null)
return null;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -64,7 +64,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
final Map<String, AlignmentContext> contexts,
final AlignmentContextUtils.ReadOrientation contextType,
final GenotypePriors priors,
final Allele alternateAlleleToUse,
final List<Allele> alternateAllelesToUse,
final boolean useBAQedPileup,
final GenomeLocParser locParser) {
@ -95,8 +95,8 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
}
// find the alternate allele(s) that we should be using
if ( alternateAlleleToUse != null ) {
alleles.add(alternateAlleleToUse);
if ( alternateAllelesToUse != null ) {
alleles.addAll(alternateAllelesToUse);
} else if ( useAlleleFromVCF ) {
final VariantContext vc = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, ref.getLocus(), true, logger, UAC.alleles);

14
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -237,14 +237,14 @@ public class UnifiedGenotyperEngine {
// ---------------------------------------------------------------------------------------------------------
// private method called by both UnifiedGenotyper and UGCalcLikelihoods entry points into the engine
private VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, Map<String, AlignmentContext> stratifiedContexts, AlignmentContextUtils.ReadOrientation type, Allele alternateAlleleToUse, boolean useBAQedPileup, final GenotypeLikelihoodsCalculationModel.Model model) {
private VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, Map<String, AlignmentContext> stratifiedContexts, AlignmentContextUtils.ReadOrientation type, List<Allele> alternateAllelesToUse, boolean useBAQedPileup, final GenotypeLikelihoodsCalculationModel.Model model) {
// initialize the data for this thread if that hasn't been done yet
if ( glcm.get() == null ) {
glcm.set(getGenotypeLikelihoodsCalculationObject(logger, UAC));
}
return glcm.get().get(model).getLikelihoods(tracker, refContext, stratifiedContexts, type, getGenotypePriors(model), alternateAlleleToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser);
return glcm.get().get(model).getLikelihoods(tracker, refContext, stratifiedContexts, type, getGenotypePriors(model), alternateAllelesToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser);
}
private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, AlignmentContext rawContext) {
@ -398,16 +398,14 @@ public class UnifiedGenotyperEngine {
//final boolean DEBUG_SLOD = false;
// the overall lod
VariantContext vcOverall = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, vc.getAlternateAllele(0), false, model);
clearAFarray(AFresult.log10AlleleFrequencyLikelihoods);
clearAFarray(AFresult.log10AlleleFrequencyPosteriors);
afcm.get().getLog10PNonRef(vcOverall, getAlleleFrequencyPriors(model), AFresult);
//double overallLog10PofNull = AFresult.log10AlleleFrequencyPosteriors[0];
double overallLog10PofF = MathUtils.log10sumLog10(AFresult.log10AlleleFrequencyPosteriors[0], 0);
//if ( DEBUG_SLOD ) System.out.println("overallLog10PofF=" + overallLog10PofF);
List<Allele> alternateAllelesToUse = builder.make().getAlternateAlleles();
// the forward lod
VariantContext vcForward = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.FORWARD, vc.getAlternateAllele(0), false, model);
VariantContext vcForward = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.FORWARD, alternateAllelesToUse, false, model);
clearAFarray(AFresult.log10AlleleFrequencyLikelihoods);
clearAFarray(AFresult.log10AlleleFrequencyPosteriors);
afcm.get().getLog10PNonRef(vcForward, getAlleleFrequencyPriors(model), AFresult);
@ -417,7 +415,7 @@ public class UnifiedGenotyperEngine {
//if ( DEBUG_SLOD ) System.out.println("forwardLog10PofNull=" + forwardLog10PofNull + ", forwardLog10PofF=" + forwardLog10PofF);
// the reverse lod
VariantContext vcReverse = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.REVERSE, vc.getAlternateAllele(0), false, model);
VariantContext vcReverse = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.REVERSE, alternateAllelesToUse, false, model);
clearAFarray(AFresult.log10AlleleFrequencyLikelihoods);
clearAFarray(AFresult.log10AlleleFrequencyPosteriors);
afcm.get().getLog10PNonRef(vcReverse, getAlleleFrequencyPriors(model), AFresult);