From e964d17518d91cb5fc46e1bd41b76a78f72a0002 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 1 May 2012 11:02:28 -0400
Subject: [PATCH] Removing public to private dependency

---
 ...ntReadsInActiveRegionsIntegrationTest.java | 44 -------------------
 1 file changed, 44 deletions(-)
 delete mode 100644 public/java/test/org/broadinstitute/sting/gatk/walkers/activeregionqc/CountReadsInActiveRegionsIntegrationTest.java

diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/activeregionqc/CountReadsInActiveRegionsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/activeregionqc/CountReadsInActiveRegionsIntegrationTest.java
deleted file mode 100644
index 250a3d368..000000000
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/activeregionqc/CountReadsInActiveRegionsIntegrationTest.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright (c) 2012, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.gatk.walkers.activeregionqc;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.testng.annotations.Test;
-
-import java.util.Arrays;
-
-/**
- * Tests CountReadsInActiveRegions
- */
-public class CountReadsInActiveRegionsIntegrationTest extends WalkerTest {
-    @Test
-    public void basicTest() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                "-T CountReadsInActiveRegions -R " + b37KGReference + " -I " + b37GoodNA12878BAM + " -L 20:10,000,000-10,200,000 -o %s",
-                1,
-                Arrays.asList("942d067e6863a3f3524f67dc0aa02ef2"));
-        executeTest("CountReadsInActiveRegions:", spec);
-    }
-}
\ No newline at end of file