From dd6d61c0311b9cf5b5ff46fb1d39edf53430109c Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Jun 2011 21:02:47 +0000
Subject: [PATCH] Adding integration test to cover the case of a read that only
 covers an insertion (i.e. no M in the CIGAR string).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5923 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/PrintReadsIntegrationTest.java  | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java
index fab628bfd..cfebfaf0f 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsIntegrationTest.java
@@ -38,5 +38,15 @@ public class PrintReadsIntegrationTest extends WalkerTest {
                 Arrays.asList(params.md5));
         executeTest("testPrintReads-"+params.args, spec).getFirst();
     }
+
+    @Test
+    public void testPrintReadsReadAllInsertion() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T PrintReads -R " + b37KGReference +
+                        " -I " + validationDataLocation + "oneReadAllInsertion.bam" +
+                        " -o %s",
+                Arrays.asList("6caec4f8a25befb6aba562955401af93"));
+        executeTest("testPrintReads-oneReadAllInsertion", spec);
+    }
 }