fixes new qual regression in 4.0.5.0 (#4980)

Author: davidbenjamin

src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculator.java

@@ -101,7 +101,10 @@ public AFCalculationResult getLog10PNonRef(final VariantContext vc, final int de
                 nonVariantIndicesByPloidy.computeIfAbsent(ploidy, p -> genotypeIndicesWithOnlyRefAndSpanDel(p, alleles));
                 final int[] nonVariantIndices = nonVariantIndicesByPloidy.get(ploidy);
                 final double[] nonVariantLog10Posteriors = MathUtils.applyToArray(nonVariantIndices, n -> log10GenotypePosteriors[n]);
-                log10PNoVariant += MathUtils.log10SumLog10(nonVariantLog10Posteriors);
+                // when the only alt allele is the spanning deletion the probability that the site is non-variant
+                // may be so close to 1 that finite precision error in log10SumLog10 yields a positive value,
+                // which is bogus.  Thus we cap it at 0.
+                log10PNoVariant += Math.min(0,MathUtils.log10SumLog10(nonVariantLog10Posteriors));
             }
 
             // per allele non-log space probabilities of zero counts for this sample

src/test/java/org/broadinstitute/hellbender/tools/walkers/genotyper/afcalc/AlleleFrequencyCalculatorUnitTest.java

@@ -178,8 +178,6 @@ public void testSpanningDeletionIsNotConsideredVariant() {
         final AlleleFrequencyCalculator afCalc = new AlleleFrequencyCalculator(1, 0.1, 0.1, ploidy);
         final List<Allele> alleles = Arrays.asList(A, B, Allele.SPAN_DEL);
 
-        //{AA}, {AB}, {BB}, {AC}, {BC}, {CC}
-
         // some pls that have high likelihood for span del allele but not for the SNP (B)
         final int[] spanDelPls = new int[] {50, 100, 100, 0, 100, 100};
 
@@ -246,6 +244,19 @@ public void testPresenceOfUnlikelySpanningDeletionDoesntAffectResults() {
         Assert.assertEquals(log10PVariantWithoutSpanDel, log10PVariantWithSpanDel, 0.0001);
     }
 
+    // test that a finite precision bug for span del sites with a very unlikely alt allele doesn't occur
+    @Test
+    public void testSpanningDeletionWithVeryUnlikelyAltAllele() {
+        final int ploidy = 4;
+        final AlleleFrequencyCalculator afCalc = new AlleleFrequencyCalculator(1, 0.1, 0.1, ploidy);
+        final List<Allele> alleles = Arrays.asList(A, Allele.SPAN_DEL, B);
+
+        // make PLs that don't support the alt allele
+        final List<int[]> pls = Arrays.asList(new int[] {0,10000,10000,10000,10000, 10000,10000,10000,10000,10000,10000,10000,10000,10000,10000});
+        final VariantContext vc = makeVC(alleles, pls.stream().map(pl -> makeGenotype(ploidy, pl)).collect(Collectors.toList()));
+        final double log10PVariant = afCalc.getLog10PNonRef(vc).getLog10LikelihoodOfAFGT0();
+    }
+
     // make PLs that correspond to an obvious call i.e. one PL is relatively big and the rest are zero
     // alleleCounts is the GenotypeAlleleCounts format for the obvious genotype, with repeats but in no particular order
     private static int[] PLsForObviousCall(final int ploidy, final int numAlleles, final int[] alleleCounts, final int PL)   {