Merge pull request #1426 from broadinstitute/ms_excessHetSmallP

Changes max value output for ExcessHet

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHet.java

@@ -139,8 +139,9 @@ public class ExcessHet extends InfoFieldAnnotation implements StandardAnnotation
         double pval = exactTest(genotypeCounts);
 
         //If the actual phredPval would be infinity we will probably still filter out just a very large number
+        //Since the method does not guarantee precision for any p-value smaller than 1e-16, we can return the phred scaled version
         if (pval == 0) {
-            return Integer.MAX_VALUE;
+            return -10.0 * Math.log10(minNeededValue);
         }
         double phredPval = -10.0 * Math.log10(pval);
 

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/ExcessHetUnitTest.java

@@ -223,6 +223,9 @@ public class ExcessHetUnitTest {
         final double EHHets = new ExcessHet().calculateEH(allHet, allHet.getGenotypes());
 
         Assert.assertTrue(Math.abs(EHsingleton) < Math.abs(EHHets), String.format("singleton=%f allHets=%f", EHsingleton, EHHets));
+
+        //Since all hets is such an extreme case and the sample size is large here, we know that the p-value should be 0
+        Assert.assertTrue(EHHets == 160.0, String.format("P-value of 0 should be phred scaled to 160.0"));
     }
 
     @DataProvider(name = "smallSets")