Major refactor/completion of new Pool Caller under UnifiedGenotyper framework. PoolAFCalculationModel implements new math to combine pools - correct, but still O(N^2) and not complete yet for multiallelics. Pool likelihoods are better encapsulated and kept in an internal hashmap from int[] -> double for space efficiency (likelihoods can be big for pool calls when in initial discovery mode with 4 alleles). Maybe need several iterations of optimization to make it runnable at large scale. Still need to correct function chooseMostLikelyAlternateAlleles before full runs can be produced.
This commit is contained in:
Guillermo del Angel
parent
4075bc7d3d
commit
9e11b4f9a7
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.io.PrintStream;
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@ -72,4 +73,17 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
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protected abstract List<Allele> getLog10PNonRef(final VariantContext vc,
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final double[] log10AlleleFrequencyPriors,
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final AlleleFrequencyCalculationResult result);
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/**
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* Must be overridden by concrete subclasses
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* @param vc variant context with alleles and genotype likelihoods
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* @param allelesToUse alleles to subset
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* @param assignGenotypes
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* @param ploidy
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* @return GenotypesContext object
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*/
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protected abstract GenotypesContext subsetAlleles(final VariantContext vc,
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final List<Allele> allelesToUse,
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final boolean assignGenotypes,
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final int ploidy);
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}
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@ -446,6 +446,12 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
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return coeff;
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}
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public GenotypesContext subsetAlleles(final VariantContext vc,
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final List<Allele> allelesToUse,
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final boolean assignGenotypes,
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final int ploidy) {
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return VariantContextUtils.subsetAlleles(vc, allelesToUse, assignGenotypes);
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}
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// -------------------------------------------------------------------------------------
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//
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@ -357,7 +357,7 @@ public class UnifiedGenotyperEngine {
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}
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// create the genotypes
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final GenotypesContext genotypes = VariantContextUtils.subsetAlleles(vc, myAlleles, true);
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final GenotypesContext genotypes = afcm.get().subsetAlleles(vc, myAlleles, true,ploidy);
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// print out stats if we have a writer
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if ( verboseWriter != null && !limitedContext )
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@ -231,7 +231,7 @@ public class GenotypeLikelihoods {
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private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALLELES_THAT_CAN_BE_GENOTYPED); // start with data for 10 alternate alleles
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private static GenotypeLikelihoodsAllelePair[] calculatePLcache(final int altAlleles) {
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final int numLikelihoods = calculateNumLikelihoods(altAlleles);
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final int numLikelihoods = calculateNumLikelihoods(1+altAlleles, 2);
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final GenotypeLikelihoodsAllelePair[] cache = new GenotypeLikelihoodsAllelePair[numLikelihoods];
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// for all possible combinations of 2 alleles
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@ -251,11 +251,22 @@ public class GenotypeLikelihoods {
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}
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// how many likelihoods are associated with the given number of alternate alleles?
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public static int calculateNumLikelihoods(final int numAltAlleles) {
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int numLikelihoods = 1;
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public static int calculateNumLikelihoods(final int numAlleles, final int ploidy) {
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if (numAlleles == 1)
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return 1;
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else if (ploidy == 1)
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return numAlleles;
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int acc =0;
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for (int k=0; k <= ploidy; k++ )
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acc += calculateNumLikelihoods(numAlleles-1, ploidy-k);
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return acc;
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/* int numLikelihoods = 1;
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for ( int i = 1; i <= numAltAlleles; i++ )
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numLikelihoods += i + 1;
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return numLikelihoods;
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return numLikelihoods; */
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}
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// As per the VCF spec: "the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j.
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@ -30,6 +30,7 @@ import org.apache.commons.jexl2.JexlEngine;
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import org.apache.log4j.Logger;
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import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
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import org.broadinstitute.sting.commandline.Hidden;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
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import org.broadinstitute.sting.utils.*;
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import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
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@ -119,7 +120,7 @@ public class VariantContextUtils {
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builder.attributes(attrs);
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}
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private static String makePrecisionFormatStringFromDenominatorValue(double maxValue) {
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public static String makePrecisionFormatStringFromDenominatorValue(double maxValue) {
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int precision = 1;
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while ( maxValue > 1 ) {
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@ -1116,7 +1117,7 @@ public class VariantContextUtils {
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altAlleleIndexToUse[i] = true;
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}
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final int numLikelihoods = GenotypeLikelihoods.calculateNumLikelihoods(numOriginalAltAlleles);
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final int numLikelihoods = GenotypeLikelihoods.calculateNumLikelihoods(numOriginalAltAlleles, UnifiedGenotyperEngine.DEFAULT_PLOIDY);
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for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) {
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final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
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// consider this entry only if both of the alleles are good
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@ -84,7 +84,7 @@ public abstract class BaseTest {
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public static final String hg19Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list";
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public static final String hg19Chr20Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list";
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public static final boolean REQUIRE_NETWORK_CONNECTION = true;
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public static final boolean REQUIRE_NETWORK_CONNECTION = false;
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public static final String networkTempDir;
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public static final File networkTempDirFile;
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