Merge pull request #12 from broadinstitute/md_exact_fast_path_GSA-726

Fast path for biallelic variants in IndependentAllelesDiploidExactAFCalc

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java

@@ -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);
 

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

@@ -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++ ) {
+        if ( nAltAlleles == 1 ) {
-            vcs.add(biallelicCombinedGLs(vc, altI + 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;
     }
 
     /**