Merge pull request #1954 from broadinstitute/ms_ExcessHetMaxVal

Changes max value output for ExcessHet
broadinstitute · Jul 1, 2016 · 0cebc03 · 0cebc03
2 parents 3f08383 + 0fe79e0
commit 0cebc03
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ExcessHet.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/ExcessHet.java
@@ -26,6 +26,7 @@
  */
 public final class ExcessHet extends InfoFieldAnnotation implements StandardAnnotation {
     private static final double MIN_NEEDED_VALUE = 1.0E-16;
+    public static final double PHRED_SCALED_MIN_P_VALUE = -10.0 * Math.log10(MIN_NEEDED_VALUE);
 
     @Override
     public Map<String, Object> annotate(final ReferenceContext ref,
@@ -58,8 +59,9 @@ Pair<Integer, Double> calculateEH(final VariantContext vc, final GenotypesContex
         final double pval = exactTest(hetCount, refCount, homCount);
 
         //If the actual phredPval would be infinity we will probably still filter out just a very large number
-        if (Math.abs(pval - 0.0) < 10e-60) {
-            return Pair.of(Integer.MAX_VALUE, Double.POSITIVE_INFINITY);
+        //Since the method does not guarantee precision for any p-value smaller than 1e-16, we can return the phred scaled version
+        if (pval < 10e-60) {
+            return Pair.of(sampleCount, PHRED_SCALED_MIN_P_VALUE);
         }
         final double phredPval = -10.0 * Math.log10(pval);
 

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ExcessHetUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/ExcessHetUnitTest.java
@@ -182,6 +182,9 @@ public void testAllHetsForLargeCohorts() {
         final double hetsValue = new ExcessHet().calculateEH(allHet, allHet.getGenotypes()).getValue();
 
         Assert.assertTrue(Math.abs(singletonValue) < Math.abs(hetsValue), String.format("singleton=%f allHets=%f", singletonValue, hetsValue));
+
+        //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.assertEquals(hetsValue, ExcessHet.PHRED_SCALED_MIN_P_VALUE, DELTA_PRECISION, String.format("P-value of 0 should be phred scaled to " + ExcessHet.PHRED_SCALED_MIN_P_VALUE));
     }
 
     @DataProvider(name = "smallSets")