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Merge pull request #12 from broadinstitute/md_exact_fast_path_GSA-726 

Fast path for biallelic variants in IndependentAllelesDiploidExactAFCalc
This commit is contained in:
eitanbanks 2013-02-06 07:43:02 -08:00
parent 584899329c 59df329776
commit bd0349e570
2 changed files with 32 additions and 13 deletions
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11
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
View File

@ -113,12 +113,14 @@ public abstract class AFCalc implements Cloneable {
/**
* Compute the probability of the alleles segregating given the genotype likelihoods of the samples in vc
*
* @param vc the VariantContext holding the alleles and sample information
* @param vc the VariantContext holding the alleles and sample information. The VariantContext
* must have at least 1 alternative allele
* @param log10AlleleFrequencyPriors a prior vector nSamples x 2 in length indicating the Pr(AF = i)
* @return result (for programming convenience)
*/
public AFCalcResult getLog10PNonRef(final VariantContext vc, final double[] log10AlleleFrequencyPriors) {
if ( vc == null ) throw new IllegalArgumentException("VariantContext cannot be null");
if ( vc.getNAlleles() == 1 ) throw new IllegalArgumentException("VariantContext has only a single reference allele, but getLog10PNonRef requires at least one at all " + vc);
if ( log10AlleleFrequencyPriors == null ) throw new IllegalArgumentException("priors vector cannot be null");
if ( stateTracker == null ) throw new IllegalArgumentException("Results object cannot be null");
@ -170,18 +172,19 @@ public abstract class AFCalc implements Cloneable {
* @param vc the initial VC provided by the caller to this AFcalculation
* @return a potentially simpler VC that's more tractable to genotype
*/
@Requires("vc != null")
@Requires({"vc != null", "vc.getNAlleles() > 1"})
@Ensures("result != null")
protected abstract VariantContext reduceScope(final VariantContext vc);
/**
* Actually carry out the log10PNonRef calculation on vc, storing results in results
*
* @param vc variant context with alleles and genotype likelihoods
* @param vc variant context with alleles and genotype likelihoods,
* must have at least one alt allele
* @param log10AlleleFrequencyPriors priors
* @return a AFCalcResult object describing the results of this calculation
*/
@Requires({"vc != null", "log10AlleleFrequencyPriors != null"})
@Requires({"vc != null", "log10AlleleFrequencyPriors != null", "vc.getNAlleles() > 1"})
protected abstract AFCalcResult computeLog10PNonRef(final VariantContext vc,
final double[] log10AlleleFrequencyPriors);

34
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
View File

@ -156,16 +156,25 @@ import java.util.*;
public AFCalcResult computeLog10PNonRef(final VariantContext vc,
final double[] log10AlleleFrequencyPriors) {
final List<AFCalcResult> independentResultTrackers = computeAlleleIndependentExact(vc, log10AlleleFrequencyPriors);
final List<AFCalcResult> withMultiAllelicPriors = applyMultiAllelicPriors(independentResultTrackers);
return combineIndependentPNonRefs(vc, withMultiAllelicPriors);
}
if ( independentResultTrackers.size() == 0 )
throw new IllegalStateException("Independent alleles model returned an empty list of results at VC " + vc);
if ( independentResultTrackers.size() == 1 ) {
// fast path for the very common bi-allelic use case
return independentResultTrackers.get(0);
} else {
// we are a multi-allelic, so we need to actually combine the results
final List<AFCalcResult> withMultiAllelicPriors = applyMultiAllelicPriors(independentResultTrackers);
return combineIndependentPNonRefs(vc, withMultiAllelicPriors);
}
}
/**
* Compute the conditional exact AFCalcResult for each allele in vc independently, returning
* the result of each, in order of the alt alleles in VC
*
* @param vc the VariantContext we want to analyze
* @param vc the VariantContext we want to analyze, with at least 1 alt allele
* @param log10AlleleFrequencyPriors the priors
* @return a list of the AFCalcResults for each bi-allelic sub context of vc
*/
@ -208,13 +217,20 @@ import java.util.*;
@Ensures("result.size() == vc.getNAlleles() - 1")
protected final List<VariantContext> makeAlleleConditionalContexts(final VariantContext vc) {
final int nAltAlleles = vc.getNAlleles() - 1;
final List<VariantContext> vcs = new LinkedList<VariantContext>();
for ( int altI = 0; altI < nAltAlleles; altI++ ) {
vcs.add(biallelicCombinedGLs(vc, altI + 1));
if ( nAltAlleles == 1 ) {
// fast path for bi-allelic case.
return Collections.singletonList(vc);
} else {
// go through the work of ripping up the VC into its biallelic components
final List<VariantContext> vcs = new LinkedList<VariantContext>();
for ( int altI = 0; altI < nAltAlleles; altI++ ) {
vcs.add(biallelicCombinedGLs(vc, altI + 1));
}
return vcs;
}
return vcs;
}
/**