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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-03-12 09:42:37 -04:00
parent 191a5860cf 04cafffaa7
commit 03223029e3
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);