From ea793d8e27712804c26c91a128d7a0508eb5e277 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 17 Apr 2012 21:21:29 -0400
Subject: [PATCH] Khalid pressured me into adding an integration test that
 makes sure we don't fail on reads with adjacent I and D events.

---
 .../genotyper/UnifiedGenotyperIntegrationTest.java        | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 015f11048..4d00f6113 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -66,6 +66,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         executeTest("test Multiple SNP alleles", spec);
     }
 
+    @Test
+    public void testBadRead() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl -NO_HEADER -glm BOTH -I " + validationDataLocation + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
+                Arrays.asList("7678827a2ee21870a41c09d28d26b996"));
+        executeTest("test bad read", spec);
+    }
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // testing compressed output