Fix AFCalcResult unit test

-- I was simply passing in the wrong values into the function.  Fixed the calls, and expanded the docs on what needs to be passed in.

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

@@ -111,11 +111,11 @@ public class AFCalcResultUnitTest extends BaseTest {
 
     @Test(enabled = true, dataProvider = "TestIsPolymorphic")
     private void testIsPolymorphic(final double pNonRef, final double pThreshold, final boolean shouldBePoly) {
-        final AFCalcResult result = makePolymorphicTestData(pNonRef);
-        final boolean actualIsPoly = result.isPolymorphic(C, Math.log10(pThreshold));
-        Assert.assertEquals(actualIsPoly, shouldBePoly,
-                "isPolymorphic with pNonRef " + pNonRef + " and threshold " + pThreshold + " returned "
-                        + actualIsPoly + " but the expected result is " + shouldBePoly);
+            final AFCalcResult result = makePolymorphicTestData(pNonRef);
+            final boolean actualIsPoly = result.isPolymorphic(C, Math.log10(1 - pThreshold));
+            Assert.assertEquals(actualIsPoly, shouldBePoly,
+                    "isPolymorphic with pNonRef " + pNonRef + " and threshold " + pThreshold + " returned "
+                            + actualIsPoly + " but the expected result is " + shouldBePoly);
     }
 
     @Test(enabled = true, dataProvider = "TestIsPolymorphic")

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

@@ -230,6 +230,9 @@ public class AFCalcResult {
      * And that log10minPNonRef is -3.
      * We are considered polymorphic since 10^-5 < 10^-3 => -5 < -3
      *
+     * Note that log10minPNonRef is really the minimum confidence, scaled as an error rate, so
+     * if you want to be 99% confidence, then log10PNonRef should be log10(0.01) = -2.
+     *
      * @param log10minPNonRef the log10 scaled min pr of being non-ref to be considered polymorphic
      *
      * @return true if there's enough confidence (relative to log10minPNonRef) to reject AF == 0