From 5ac9af472cadad121a09949871382f6dac43df02 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 28 Feb 2011 19:48:56 +0000
Subject: [PATCH] Adding performance test for case with very high coverage (>
 600,000x) over an interval

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5336 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../indels/IndelRealignerPerformanceTest.java     | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
index f32a2b156..df90554a9 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
@@ -6,6 +6,21 @@ import org.testng.annotations.Test;
 import java.util.ArrayList;
 
 public class IndelRealignerPerformanceTest extends WalkerTest {
+    @Test
+    public void testHighCoverage() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+
+                "-R " + b36KGReference +
+                        " -T IndelRealigner" +
+                        " -I " + validationDataLocation + "indelRealignerTest.pilot1.veryHighCoverage.bam" +
+                        " -L 20:49,500-55,500" +
+                        " -o /dev/null" +
+                        " -targetIntervals " + validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals",
+                 0,
+                new ArrayList<String>(0));
+        executeTest("testIndelRealignerHighCoverage", spec);
+    }
+
     @Test
     public void testRealigner() {
         WalkerTestSpec spec1 = new WalkerTestSpec(