CountReadsInActiveRegions now emits a detailed GATK report

-- This report details which intervals are coming in and how many reads they contain
-- Added integration test to verify that the intervals aren't changing, before heading into the ART refactor

public/java/test/org/broadinstitute/sting/gatk/walkers/activeregionqc/CountReadsInActiveRegionsIntegrationTest.java

@@ -0,0 +1,44 @@
+/*
+ * 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("fcd581aa6befe85c7297509fa7b34edf"));
+        executeTest("CountReadsInActiveRegions:", spec);
+    }
+}