Bugfixes to make new AFCalc system pass integrationtests

-- GeneralPloidyExactAFCalc turns -Infinity values into -Double.MAX_VALUE, so our calculations pass unit tests
-- Bugfix for GeneralPloidyGenotypeLikelihoodsCalculationModel, return a null VC when the only allele we get from our final alleles to use method is the reference base
-- Fix calculation of reference posteriors when P(AF == 0) = 0.0 and P(AF == 0) = X for some meaningful value of X.  Added unit test to ensure this behavior is correct
-- Fix horrible sorting bug in IndependentAllelesDiploidExactAFCalc that applied the theta^N priors in the wrong order.  Add contract to ensure this doesn't ever happen again
-- Bugfix in GLBasedSampleSelector, where VCs without any polymorphic alleles were being sent to the exact model
--

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java

@@ -245,7 +245,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
 
         // find the alternate allele(s) that we should be using
         final List<Allele> alleles = getFinalAllelesToUse(tracker, ref, allAllelesToUse, GLs);
-        if (alleles == null || alleles.isEmpty())
+        if (alleles == null || alleles.isEmpty() || (alleles.size() == 1 && alleles.get(0).isReference()))
             return null;
         // start making the VariantContext
         final GenomeLoc loc = ref.getLocus();

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

@@ -448,7 +448,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
         // update the MLE if necessary
         final int altCounts[] = Arrays.copyOfRange(set.getACcounts().getCounts(),1, set.getACcounts().getCounts().length);
         // TODO -- GUILLERMO THIS CODE MAY PRODUCE POSITIVE LIKELIHOODS OR -INFINITY
-        getStateTracker().updateMLEifNeeded(MathUtils.goodLog10Probability(log10LofK) ? log10LofK : MathUtils.LOG10_P_OF_ZERO, altCounts);
+        getStateTracker().updateMLEifNeeded(Math.max(Math.min(log10LofK, 0.0), -Double.MAX_VALUE), altCounts);
 
         // apply the priors over each alternate allele
         for (final int ACcount : altCounts ) {
@@ -456,7 +456,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
                 log10LofK += log10AlleleFrequencyPriors[ACcount];
         }
         // TODO -- GUILLERMO THIS CODE MAY PRODUCE POSITIVE LIKELIHOODS OR -INFINITY
-        getStateTracker().updateMAPifNeeded(MathUtils.goodLog10Probability(log10LofK) ? log10LofK : MathUtils.LOG10_P_OF_ZERO, altCounts);
+        getStateTracker().updateMAPifNeeded(Math.max(Math.min(log10LofK, 0.0), -Double.MAX_VALUE), altCounts);
 
         return log10LofK;
     }

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java

@@ -56,6 +56,11 @@ public class AFCalcResultUnitTest extends BaseTest {
             tests.add(new Object[]{new MyTest(new double[]{-1e-9, badL}, new double[]{0.0, badL})});
         }
 
+        // test that a non-ref site gets reasonable posteriors with an ~0.0 value doesn't get lost
+        for ( final double nonRefL : Arrays.asList(-100.0, -50.0, -10.0, -9.0, -8.0, -7.0, -6.0, -5.0)) {
+            tests.add(new Object[]{new MyTest(new double[]{0.0, nonRefL}, new double[]{0.0, nonRefL})});
+        }
+
         return tests.toArray(new Object[][]{});
     }
 

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java

@@ -185,7 +185,7 @@ public class AFCalcUnitTest extends BaseTest {
             testResultSimple(cfg);
     }
 
-    @Test(enabled = true, dataProvider = "badGLs")
+    @Test(enabled = true && !DEBUG_ONLY, dataProvider = "badGLs")
     public void testBadGLs(GetGLsTest cfg) {
         testResultSimple(cfg);
     }

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

@@ -100,7 +100,7 @@ import java.util.*;
     private final static class CompareAFCalcResultsByPNonRef implements Comparator<AFCalcResult> {
         @Override
         public int compare(AFCalcResult o1, AFCalcResult o2) {
-            return Double.compare(o1.getLog10PosteriorOfAFGT0(), o2.getLog10PosteriorOfAFGT0());
+            return -1 * Double.compare(o1.getLog10PosteriorOfAFGT0(), o2.getLog10PosteriorOfAFGT0());
         }
     }
 
@@ -313,6 +313,7 @@ import java.util.*;
      *
      * @param sortedResultsWithThetaNPriors the pNonRef result for each allele independently
      */
+    @Requires("sortedByPosteriorGT(sortedResultsWithThetaNPriors)")
     protected AFCalcResult combineIndependentPNonRefs(final VariantContext vc,
                                                       final List<AFCalcResult> sortedResultsWithThetaNPriors) {
         int nEvaluations = 0;
@@ -321,8 +322,9 @@ import java.util.*;
         final double[] log10PriorsOfAC = new double[2];
         final Map<Allele, Double> log10pNonRefByAllele = new HashMap<Allele, Double>(nAltAlleles);
 
-        // this value is a sum in log space
+        // the sum of the log10 posteriors for AF == 0 and AF > 0 to determine joint probs
         double log10PosteriorOfACEq0Sum = 0.0;
+        double log10PosteriorOfACGt0Sum = 0.0;
 
         for ( final AFCalcResult sortedResultWithThetaNPriors : sortedResultsWithThetaNPriors ) {
             final Allele altAllele = sortedResultWithThetaNPriors.getAllelesUsedInGenotyping().get(1);
@@ -337,6 +339,7 @@ import java.util.*;
             // the AF > 0 case requires us to store the normalized likelihood for later summation
             if ( sortedResultWithThetaNPriors.getLog10PosteriorOfAFGT0() > MIN_LOG10_CONFIDENCE_TO_INCLUDE_ALLELE_IN_POSTERIOR )
                 log10PosteriorOfACEq0Sum += sortedResultWithThetaNPriors.getLog10PosteriorOfAFEq0();
+            log10PosteriorOfACGt0Sum += sortedResultWithThetaNPriors.getLog10PosteriorOfAFGT0();
 
             // bind pNonRef for allele to the posterior value of the AF > 0 with the new adjusted prior
             log10pNonRefByAllele.put(altAllele, sortedResultWithThetaNPriors.getLog10PosteriorOfAFGT0());
@@ -348,7 +351,16 @@ import java.util.*;
         // In principle, if B_p = x and C_p = y are the probabilities of being poly for alleles B and C,
         // the probability of being poly is (1 - B_p) * (1 - C_p) = (1 - x) * (1 - y).  We want to estimate confidently
         // log10((1 - x) * (1 - y)) which is log10(1 - x) + log10(1 - y).  This sum is log10PosteriorOfACEq0
-        final double log10PosteriorOfACGt0 = Math.max(Math.log10(1 - Math.pow(10, log10PosteriorOfACEq0Sum)), MathUtils.LOG10_P_OF_ZERO);
+        //
+        // note we need to handle the case where the posterior of AF == 0 is 0.0, in which case we
+        // use the summed log10PosteriorOfACGt0Sum directly.  This happens in cases where
+        //   AF > 0 : 0.0 and AF == 0 : -16, and if you use the inverse calculation you get 0.0 and MathUtils.LOG10_P_OF_ZERO
+        final double log10PosteriorOfACGt0;
+        if ( log10PosteriorOfACEq0Sum == 0.0 )
+            log10PosteriorOfACGt0 = log10PosteriorOfACGt0Sum;
+        else
+            log10PosteriorOfACGt0 = Math.max(Math.log10(1 - Math.pow(10, log10PosteriorOfACEq0Sum)), MathUtils.LOG10_P_OF_ZERO);
+
         final double[] log10LikelihoodsOfAC = new double[] {
                 // L + prior = posterior => L = poster - prior
                 log10PosteriorOfACEq0Sum - log10PriorsOfAC[0],
@@ -362,4 +374,14 @@ import java.util.*;
                 MathUtils.normalizeFromLog10(log10PriorsOfAC, true),
                 log10pNonRefByAllele, sortedResultsWithThetaNPriors);
     }
+
+    private static boolean sortedByPosteriorGT(final List<AFCalcResult> sortedVCs) {
+        double lastPosteriorGt0 = sortedVCs.get(0).getLog10PosteriorOfAFGT0();
+        for ( final AFCalcResult vc : sortedVCs ) {
+            if ( vc.getLog10PosteriorOfAFGT0() > lastPosteriorGt0 )
+                return false;
+            lastPosteriorGt0 = vc.getLog10PosteriorOfAFGT0();
+        }
+        return true;
+    }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java

@@ -48,6 +48,9 @@ public class GLBasedSampleSelector extends SampleSelector {
         // first subset to the samples
         VariantContext subContext = vc.subContextFromSamples(samples);
 
+        if ( ! subContext.isPolymorphicInSamples() )
+            return false;
+
         // now check to see (using EXACT model) whether this should be variant
         // do we want to apply a prior? maybe user-spec?
         if ( flatPriors == null ) {