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AFCR made public (for use in VSS) 

Minor changes to ValidationSiteSelector logic (SampleSelectors determine whether a site is valid for output, no actual subset context need be operated on beyond that determination). Implementation of GL-based site selection. Minor changes to EJG.
This commit is contained in:
Christopher Hartl 2011-12-19 23:14:26 -05:00
parent 339ef92eac
commit 67298f8a11
9 changed files with 74 additions and 27 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationResult.java
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@ -48,8 +48,16 @@ public class AlleleFrequencyCalculationResult {
double log10LikelihoodOfAFzero = 0.0;
double log10PosteriorOfAFzero = 0.0;
AlleleFrequencyCalculationResult(int maxAltAlleles, int numChr) {
public AlleleFrequencyCalculationResult(int maxAltAlleles, int numChr) {
log10AlleleFrequencyLikelihoods = new double[maxAltAlleles][numChr+1];
log10AlleleFrequencyPosteriors = new double[maxAltAlleles][numChr+1];
}
public double getLog10LikelihoodOfAFzero() {
return log10LikelihoodOfAFzero;
}
public double getLog10PosteriorOfAFzero() {
return log10PosteriorOfAFzero;
}
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
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@ -38,10 +38,10 @@ public abstract class FrequencyModeSelector implements Cloneable{
protected FrequencyModeSelector(GenomeLocParser parser) {
this.parser = parser;
}
protected void logCurrentSiteData(VariantContext vc, VariantContext subVC) {
logCurrentSiteData(vc, subVC, false, false);
protected void logCurrentSiteData(VariantContext vc, boolean passesCriteria) {
logCurrentSiteData(vc, passesCriteria, false, false);
}
protected abstract void logCurrentSiteData(VariantContext vc, VariantContext subVC, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC);
protected abstract void logCurrentSiteData(VariantContext vc, boolean included, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC);
protected abstract ArrayList<VariantContext> selectValidationSites(int numValidationSites);
}

43
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java
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@ -23,21 +23,52 @@
*/
package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
import org.broadinstitute.sting.gatk.walkers.genotyper.AlleleFrequencyCalculationResult;
import org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeSet;
public class GLBasedSampleSelector extends SampleSelector {
public GLBasedSampleSelector(TreeSet<String> sm) {
Map<Integer,double[][]> numAllelePriorMatrix = new HashMap<Integer,double[][]>();
double referenceLikelihood;
public GLBasedSampleSelector(TreeSet<String> sm, double refLik) {
super(sm);
referenceLikelihood = refLik;
}
public VariantContext subsetSiteToSamples(VariantContext vc) {
/* todo - Look at sample array, and create a new vc with samples for which GL's indicate they should be included.
For example, include all samples (and corresponding genotypes) whose GL's are such that argmax(GL) = HET or HOMVAR. */
throw new ReviewedStingException("GLBasedSampleSelector not implemented yet!");
//return true;
public boolean selectSiteInSamples(VariantContext vc) {
if ( samples == null || samples.isEmpty() )
return true;
// want to include a site in the given samples if it is *likely* to be variant (via the EXACT model)
// first subset to the samples
VariantContext subContext = vc.subContextFromSamples(samples);
// now check to see (using EXACT model) whether this should be variant
// do we want to apply a prior? maybe user-spec?
double[][] flatPrior = createFlatPrior(vc.getAlleles());
AlleleFrequencyCalculationResult result = new AlleleFrequencyCalculationResult(vc.getAlternateAlleles().size(),2*samples.size());
ExactAFCalculationModel.linearExactMultiAllelic(subContext.getGenotypes(),vc.getAlternateAlleles().size(),flatPrior,result,true);
// do we want to let this qual go up or down?
if ( result.getLog10PosteriorOfAFzero() < referenceLikelihood ) {
return true;
}
return false;
}
private double[][] createFlatPrior(List<Allele> alleles) {
if ( ! numAllelePriorMatrix.containsKey(alleles.size()) ) {
numAllelePriorMatrix.put(alleles.size(), new double[alleles.size()][1+2*samples.size()]);
}
return numAllelePriorMatrix.get(alleles.size());
}
}

10
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
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@ -38,14 +38,18 @@ public class GTBasedSampleSelector extends SampleSelector{
super(sm);
}
public VariantContext subsetSiteToSamples(VariantContext vc) {
public boolean selectSiteInSamples(VariantContext vc) {
// Super class already defined initialization which filled data structure "samples" with desired samples.
// We only need to check if current vc if polymorphic in that set of samples
if ( samples == null || samples.isEmpty() )
return vc;
return true;
return vc.subContextFromSamples(samples, vc.getAlleles());
VariantContext subContext = vc.subContextFromSamples(samples, vc.getAlleles());
if ( subContext.isPolymorphicInSamples() ) {
return true;
}
return false;
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
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@ -60,7 +60,7 @@ public class KeepAFSpectrumFrequencySelector extends FrequencyModeSelector {
postSampleSelectionHistogram = new int[NUM_BINS];
}
public void logCurrentSiteData(VariantContext vc, VariantContext subVC, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC) {
public void logCurrentSiteData(VariantContext vc, boolean selectedInTargetSamples, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC) {
// this method is called for every variant of a selected type, regardless of whether it will be selectable or not
// get AC,AF,AN attributes from vc
@ -107,7 +107,7 @@ public class KeepAFSpectrumFrequencySelector extends FrequencyModeSelector {
numTotalSites++;
// now process VC subsetted to samples of interest
if (!subVC.isPolymorphicInSamples() && !IGNORE_POLYMORPHIC)
if (! selectedInTargetSamples && !IGNORE_POLYMORPHIC)
return;
//System.out.format("Post:%4.4f %d\n",af0, binIndex);

5
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
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@ -33,8 +33,7 @@ public class NullSampleSelector extends SampleSelector{
super(sm);
}
public VariantContext subsetSiteToSamples(VariantContext vc) {
return vc;
public boolean selectSiteInSamples(VariantContext vc) {
return true;
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
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@ -34,7 +34,7 @@ public abstract class SampleSelector implements Cloneable {
samples = new TreeSet<String>(sm);
}
protected abstract VariantContext subsetSiteToSamples(VariantContext vc);
protected abstract boolean selectSiteInSamples(VariantContext vc);
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
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@ -42,14 +42,14 @@ public class UniformSamplingFrequencySelector extends FrequencyModeSelector {
}
public void logCurrentSiteData(VariantContext vc, VariantContext subVC, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC) {
public void logCurrentSiteData(VariantContext vc, boolean selectedInTargetSamples, boolean IGNORE_GENOTYPES, boolean IGNORE_POLYMORPHIC) {
HashMap<String, Object> attributes = new HashMap<String, Object>();
if (vc.hasGenotypes() && !IGNORE_GENOTYPES) {
// recompute AF,AC,AN based on genotypes:
VariantContextUtils.calculateChromosomeCounts(vc, attributes, false);
if (!subVC.isPolymorphicInSamples() && !IGNORE_POLYMORPHIC)
if (! selectedInTargetSamples && !IGNORE_POLYMORPHIC)
return;
} else {
if ( attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY) ) {

17
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelectorWalker.java
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@ -124,6 +124,10 @@ public class ValidationSiteSelectorWalker extends RodWalker<Integer, Integer> {
@Argument(fullName="sampleMode", shortName="sampleMode", doc="Sample selection mode", required=false)
private SAMPLE_SELECTION_MODE sampleMode = SAMPLE_SELECTION_MODE.NONE;
@Argument(shortName="samplePNonref",fullName="samplePNonref", doc="GL-based selection mode only: the probability" +
" that a site is non-reference in the samples for which to include the site",required=false)
private double samplePNonref = 0.99;
@Argument(fullName="numValidationSites", shortName="numSites", doc="Number of output validation sites", required=true)
private int numValidationSites;
@ -231,13 +235,14 @@ public class ValidationSiteSelectorWalker extends RodWalker<Integer, Integer> {
continue;
// do anything required by frequency selector before we select for samples
VariantContext subVC;
// does this site pass the criteria for the samples we are interested in?
boolean passesSampleSelectionCriteria;
if (samples.isEmpty())
subVC = vc;
passesSampleSelectionCriteria = true;
else
subVC = sampleSelector.subsetSiteToSamples(vc);
frequencyModeSelector.logCurrentSiteData(vc, subVC, IGNORE_GENOTYPES, IGNORE_POLYMORPHIC);
passesSampleSelectionCriteria = sampleSelector.selectSiteInSamples(vc);
frequencyModeSelector.logCurrentSiteData(vc,passesSampleSelectionCriteria,IGNORE_GENOTYPES,IGNORE_POLYMORPHIC);
}
return 1;
}
@ -263,7 +268,7 @@ public class ValidationSiteSelectorWalker extends RodWalker<Integer, Integer> {
SampleSelector sm;
switch ( sampleMode ) {
case POLY_BASED_ON_GL:
sm = new GLBasedSampleSelector(samples);
sm = new GLBasedSampleSelector(samples, Math.log10(1.0-samplePNonref));
break;
case POLY_BASED_ON_GT:
sm = new GTBasedSampleSelector(samples);