From 849a2b883950abc25d8390aecc69de7a5d44c167 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Wed, 12 Sep 2012 12:23:00 -0400
Subject: [PATCH] Adding HC integration test for _structural_ insertions and
 deletions.

---
 .../haplotypecaller/HaplotypeCallerIntegrationTest.java   | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
index b45c027a7..b4ac2b86d 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -73,4 +73,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
         final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("8d092b25f40456e618eef91fdce8adf0"));
         executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
     }
+
+    @Test
+    public void HCTestStructuralIndels() {
+        final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c29e61810c056b52a47baae0696931ea"));
+        executeTest("HCTestStructuralIndels: ", spec);
+    }
+
 }