From 297afc79119cfd6c0def1063b9e005c8b7ab6b70 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 12 Apr 2012 15:43:14 -0400
Subject: [PATCH] Added unit test to ensure that we genotype correctly cases
 with really large GLs

---
 .../genotyper/ExactAFCalculationModelUnitTest.java | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModelUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModelUnitTest.java
index 31c7a4e83..964d768c4 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModelUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModelUnitTest.java
@@ -94,4 +94,18 @@ public class ExactAFCalculationModelUnitTest extends BaseTest {
             Assert.assertEquals(calculatedAlleleCount, expectedAlleleCount);
         }
     }
+
+    @Test
+    public void testLargeGLs() {
+
+        final double[] BB = new double[]{-20000000.0, -20000000.0, 0.0};
+        GetGLsTest cfg = new GetGLsTest("B6", 1, createGenotype("1", BB), createGenotype("2", BB), createGenotype("3", BB));
+
+        final AlleleFrequencyCalculationResult result = new AlleleFrequencyCalculationResult(2);
+
+        ExactAFCalculationModel.linearExactMultiAllelic(cfg.GLs, cfg.numAltAlleles, priors, result);
+
+        int calculatedAlleleCount = result.getAlleleCountsOfMAP()[0];
+        Assert.assertEquals(calculatedAlleleCount, 6);
+    }
 }