Move the code to subset a Variant Context to fewer alleles (including restructuring the PLs appropriately) into VariantContextUtils where it can be used generally.
This commit is contained in:
Eric Banks
parent
a0843f125e
commit
e4a225ed09
|
|
@ -56,7 +56,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
|
|||
alleles = new ArrayList<Allele>(MAX_ALTERNATE_ALLELES_TO_GENOTYPE + 1);
|
||||
alleles.add(vc.getReference());
|
||||
alleles.addAll(chooseMostLikelyAlternateAlleles(vc, MAX_ALTERNATE_ALLELES_TO_GENOTYPE));
|
||||
GLs = UnifiedGenotyperEngine.subsetAlleles(vc, alleles, false);
|
||||
GLs = VariantContextUtils.subsetAlleles(vc, alleles, false);
|
||||
}
|
||||
|
||||
linearExactMultiAllelic(GLs, alleles.size() - 1, log10AlleleFrequencyPriors, result);
|
||||
|
|
@ -120,7 +120,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
|
|||
if ( sample.hasLikelihoods() ) {
|
||||
double[] gls = sample.getLikelihoods().getAsVector();
|
||||
|
||||
if ( MathUtils.sum(gls) < UnifiedGenotyperEngine.SUM_GL_THRESH_NOCALL )
|
||||
if ( MathUtils.sum(gls) < VariantContextUtils.SUM_GL_THRESH_NOCALL )
|
||||
genotypeLikelihoods.add(gls);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -61,10 +61,6 @@ public class UnifiedGenotyperEngine {
|
|||
* mutations (SNPs) in DISCOVERY mode or generally when running in GENOTYPE_GIVEN_ALLELES mode; it will by
|
||||
* no means produce a comprehensive set of indels in DISCOVERY mode */
|
||||
EMIT_ALL_SITES
|
||||
}
|
||||
|
||||
protected static final List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
|
||||
protected static final double SUM_GL_THRESH_NOCALL = -0.001; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
|
||||
|
||||
// the unified argument collection
|
||||
private final UnifiedArgumentCollection UAC;
|
||||
|
|
@ -348,7 +344,7 @@ public class UnifiedGenotyperEngine {
|
|||
}
|
||||
|
||||
// create the genotypes
|
||||
final GenotypesContext genotypes = subsetAlleles(vc, myAlleles, true);
|
||||
final GenotypesContext genotypes = VariantContextUtils.subsetAlleles(vc, myAlleles, true);
|
||||
|
||||
// print out stats if we have a writer
|
||||
if ( verboseWriter != null && !limitedContext )
|
||||
|
|
@ -730,116 +726,4 @@ public class UnifiedGenotyperEngine {
|
|||
|
||||
return vc;
|
||||
}
|
||||
|
||||
/**
|
||||
* @param vc variant context with genotype likelihoods
|
||||
* @return genotypes
|
||||
*/
|
||||
public static GenotypesContext assignGenotypes(final VariantContext vc) {
|
||||
return subsetAlleles(vc, vc.getAlleles(), true);
|
||||
}
|
||||
|
||||
/**
|
||||
* @param vc variant context with genotype likelihoods
|
||||
* @param allelesToUse which alleles from the vc are okay to use; *** must be in the same relative order as those in the original VC ***
|
||||
* @param assignGenotypes true if we should change the genotypes based on the (subsetted) PLs
|
||||
* @return genotypes
|
||||
*/
|
||||
public static GenotypesContext subsetAlleles(final VariantContext vc,
|
||||
final List<Allele> allelesToUse,
|
||||
final boolean assignGenotypes) {
|
||||
|
||||
// the genotypes with PLs
|
||||
final GenotypesContext oldGTs = vc.getGenotypes();
|
||||
|
||||
// samples
|
||||
final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();
|
||||
|
||||
// the new genotypes to create
|
||||
final GenotypesContext newGTs = GenotypesContext.create();
|
||||
|
||||
// we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
|
||||
final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
|
||||
final int numNewAltAlleles = allelesToUse.size() - 1;
|
||||
|
||||
// which PLs should be carried forward?
|
||||
ArrayList<Integer> likelihoodIndexesToUse = null;
|
||||
|
||||
// an optimization: if we are supposed to use all (or none in the case of a ref call) of the alleles,
|
||||
// then we can keep the PLs as is; otherwise, we determine which ones to keep
|
||||
if ( numNewAltAlleles != numOriginalAltAlleles && numNewAltAlleles > 0 ) {
|
||||
likelihoodIndexesToUse = new ArrayList<Integer>(30);
|
||||
|
||||
final boolean[] altAlleleIndexToUse = new boolean[numOriginalAltAlleles];
|
||||
for ( int i = 0; i < numOriginalAltAlleles; i++ ) {
|
||||
if ( allelesToUse.contains(vc.getAlternateAllele(i)) )
|
||||
altAlleleIndexToUse[i] = true;
|
||||
}
|
||||
|
||||
final int numLikelihoods = GenotypeLikelihoods.calculateNumLikelihoods(numOriginalAltAlleles);
|
||||
for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) {
|
||||
final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
|
||||
// consider this entry only if both of the alleles are good
|
||||
if ( (alleles.alleleIndex1 == 0 || altAlleleIndexToUse[alleles.alleleIndex1 - 1]) && (alleles.alleleIndex2 == 0 || altAlleleIndexToUse[alleles.alleleIndex2 - 1]) )
|
||||
likelihoodIndexesToUse.add(PLindex);
|
||||
}
|
||||
}
|
||||
|
||||
// create the new genotypes
|
||||
for ( int k = 0; k < oldGTs.size(); k++ ) {
|
||||
final Genotype g = oldGTs.get(sampleIndices.get(k));
|
||||
if ( !g.hasLikelihoods() ) {
|
||||
newGTs.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, Genotype.NO_LOG10_PERROR, null, null, false));
|
||||
continue;
|
||||
}
|
||||
|
||||
// create the new likelihoods array from the alleles we are allowed to use
|
||||
final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
|
||||
double[] newLikelihoods;
|
||||
if ( likelihoodIndexesToUse == null ) {
|
||||
newLikelihoods = originalLikelihoods;
|
||||
} else {
|
||||
newLikelihoods = new double[likelihoodIndexesToUse.size()];
|
||||
int newIndex = 0;
|
||||
for ( int oldIndex : likelihoodIndexesToUse )
|
||||
newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];
|
||||
|
||||
// might need to re-normalize
|
||||
newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
|
||||
}
|
||||
|
||||
// if there is no mass on the (new) likelihoods, then just no-call the sample
|
||||
if ( MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) {
|
||||
newGTs.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, Genotype.NO_LOG10_PERROR, null, null, false));
|
||||
}
|
||||
else {
|
||||
Map<String, Object> attrs = new HashMap<String, Object>(g.getAttributes());
|
||||
if ( numNewAltAlleles == 0 )
|
||||
attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
|
||||
else
|
||||
attrs.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(newLikelihoods));
|
||||
|
||||
// if we weren't asked to assign a genotype, then just no-call the sample
|
||||
if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL )
|
||||
newGTs.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, Genotype.NO_LOG10_PERROR, null, attrs, false));
|
||||
else
|
||||
newGTs.add(assignGenotype(g, newLikelihoods, allelesToUse, numNewAltAlleles, attrs));
|
||||
}
|
||||
}
|
||||
|
||||
return newGTs;
|
||||
}
|
||||
|
||||
protected static Genotype assignGenotype(final Genotype originalGT, final double[] newLikelihoods, final List<Allele> allelesToUse, final int numNewAltAlleles, final Map<String, Object> attrs) {
|
||||
// find the genotype with maximum likelihoods
|
||||
int PLindex = numNewAltAlleles == 0 ? 0 : MathUtils.maxElementIndex(newLikelihoods);
|
||||
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
|
||||
|
||||
ArrayList<Allele> myAlleles = new ArrayList<Allele>();
|
||||
myAlleles.add(allelesToUse.get(alleles.alleleIndex1));
|
||||
myAlleles.add(allelesToUse.get(alleles.alleleIndex2));
|
||||
|
||||
final double qual = numNewAltAlleles == 0 ? Genotype.NO_LOG10_PERROR : GenotypeLikelihoods.getQualFromLikelihoods(PLindex, newLikelihoods);
|
||||
return new Genotype(originalGT.getSampleName(), myAlleles, qual, null, attrs, false);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -30,10 +30,7 @@ import org.apache.commons.jexl2.JexlEngine;
|
|||
import org.apache.log4j.Logger;
|
||||
import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
|
||||
import org.broadinstitute.sting.commandline.Hidden;
|
||||
import org.broadinstitute.sting.utils.BaseUtils;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.GenomeLocParser;
|
||||
import org.broadinstitute.sting.utils.Utils;
|
||||
import org.broadinstitute.sting.utils.*;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
|
|
@ -1066,4 +1063,135 @@ public class VariantContextUtils {
|
|||
names.add(g.getSampleName());
|
||||
return names;
|
||||
}
|
||||
|
||||
/**
|
||||
* Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs
|
||||
*
|
||||
* @param vc variant context with genotype likelihoods
|
||||
* @return genotypes context
|
||||
*/
|
||||
public static GenotypesContext assignGenotypes(final VariantContext vc) {
|
||||
return subsetAlleles(vc, vc.getAlleles(), true);
|
||||
}
|
||||
|
||||
private static final List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
|
||||
public static final double SUM_GL_THRESH_NOCALL = -0.001; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
|
||||
|
||||
/**
|
||||
* subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately)
|
||||
*
|
||||
* @param vc variant context with genotype likelihoods
|
||||
* @param allelesToUse which alleles from the vc are okay to use; *** must be in the same relative order as those in the original VC ***
|
||||
* @param assignGenotypes true if we should update the genotypes based on the (subsetted) PLs
|
||||
* @return genotypes
|
||||
*/
|
||||
public static GenotypesContext subsetAlleles(final VariantContext vc,
|
||||
final List<Allele> allelesToUse,
|
||||
final boolean assignGenotypes) {
|
||||
|
||||
// the genotypes with PLs
|
||||
final GenotypesContext oldGTs = vc.getGenotypes();
|
||||
|
||||
// samples
|
||||
final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();
|
||||
|
||||
// the new genotypes to create
|
||||
final GenotypesContext newGTs = GenotypesContext.create();
|
||||
|
||||
// we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
|
||||
final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
|
||||
final int numNewAltAlleles = allelesToUse.size() - 1;
|
||||
|
||||
// which PLs should be carried forward?
|
||||
ArrayList<Integer> likelihoodIndexesToUse = null;
|
||||
|
||||
// an optimization: if we are supposed to use all (or none in the case of a ref call) of the alleles,
|
||||
// then we can keep the PLs as is; otherwise, we determine which ones to keep
|
||||
if ( numNewAltAlleles != numOriginalAltAlleles && numNewAltAlleles > 0 ) {
|
||||
likelihoodIndexesToUse = new ArrayList<Integer>(30);
|
||||
|
||||
final boolean[] altAlleleIndexToUse = new boolean[numOriginalAltAlleles];
|
||||
for ( int i = 0; i < numOriginalAltAlleles; i++ ) {
|
||||
if ( allelesToUse.contains(vc.getAlternateAllele(i)) )
|
||||
altAlleleIndexToUse[i] = true;
|
||||
}
|
||||
|
||||
final int numLikelihoods = GenotypeLikelihoods.calculateNumLikelihoods(numOriginalAltAlleles);
|
||||
for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) {
|
||||
final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
|
||||
// consider this entry only if both of the alleles are good
|
||||
if ( (alleles.alleleIndex1 == 0 || altAlleleIndexToUse[alleles.alleleIndex1 - 1]) && (alleles.alleleIndex2 == 0 || altAlleleIndexToUse[alleles.alleleIndex2 - 1]) )
|
||||
likelihoodIndexesToUse.add(PLindex);
|
||||
}
|
||||
}
|
||||
|
||||
// create the new genotypes
|
||||
for ( int k = 0; k < oldGTs.size(); k++ ) {
|
||||
final Genotype g = oldGTs.get(sampleIndices.get(k));
|
||||
if ( !g.hasLikelihoods() ) {
|
||||
newGTs.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, Genotype.NO_LOG10_PERROR, null, null, false));
|
||||
continue;
|
||||
}
|
||||
|
||||
// create the new likelihoods array from the alleles we are allowed to use
|
||||
final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
|
||||
double[] newLikelihoods;
|
||||
if ( likelihoodIndexesToUse == null ) {
|
||||
newLikelihoods = originalLikelihoods;
|
||||
} else {
|
||||
newLikelihoods = new double[likelihoodIndexesToUse.size()];
|
||||
int newIndex = 0;
|
||||
for ( int oldIndex : likelihoodIndexesToUse )
|
||||
newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];
|
||||
|
||||
// might need to re-normalize
|
||||
newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
|
||||
}
|
||||
|
||||
// if there is no mass on the (new) likelihoods, then just no-call the sample
|
||||
if ( MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) {
|
||||
newGTs.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, Genotype.NO_LOG10_PERROR, null, null, false));
|
||||
}
|
||||
else {
|
||||
Map<String, Object> attrs = new HashMap<String, Object>(g.getAttributes());
|
||||
if ( numNewAltAlleles == 0 )
|
||||
attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
|
||||
else
|
||||
attrs.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(newLikelihoods));
|
||||
|
||||
// if we weren't asked to assign a genotype, then just no-call the sample
|
||||
if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL )
|
||||
newGTs.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, Genotype.NO_LOG10_PERROR, null, attrs, false));
|
||||
else
|
||||
newGTs.add(assignGenotype(g, newLikelihoods, allelesToUse, attrs));
|
||||
}
|
||||
}
|
||||
|
||||
return newGTs;
|
||||
}
|
||||
|
||||
/**
|
||||
* Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs
|
||||
*
|
||||
* @param originalGT the original genotype
|
||||
* @param newLikelihoods the PL array
|
||||
* @param allelesToUse the list of alleles to choose from (corresponding to the PLs)
|
||||
* @param attrs the annotations to use when creating the genotype
|
||||
*
|
||||
* @return genotype
|
||||
*/
|
||||
private static Genotype assignGenotype(final Genotype originalGT, final double[] newLikelihoods, final List<Allele> allelesToUse, final Map<String, Object> attrs) {
|
||||
final int numNewAltAlleles = allelesToUse.size() - 1;
|
||||
|
||||
// find the genotype with maximum likelihoods
|
||||
int PLindex = numNewAltAlleles == 0 ? 0 : MathUtils.maxElementIndex(newLikelihoods);
|
||||
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
|
||||
|
||||
ArrayList<Allele> myAlleles = new ArrayList<Allele>();
|
||||
myAlleles.add(allelesToUse.get(alleles.alleleIndex1));
|
||||
myAlleles.add(allelesToUse.get(alleles.alleleIndex2));
|
||||
|
||||
final double qual = numNewAltAlleles == 0 ? Genotype.NO_LOG10_PERROR : GenotypeLikelihoods.getQualFromLikelihoods(PLindex, newLikelihoods);
|
||||
return new Genotype(originalGT.getSampleName(), myAlleles, qual, null, attrs, false);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue