Basic integration test for the aligner.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2131 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java

@@ -0,0 +1,29 @@
+package org.broadinstitute.sting.alignment;
+
+import org.junit.Test;
+import org.broadinstitute.sting.WalkerTest;
+
+import java.util.Arrays;
+import java.util.List;
+import java.io.File;
+
+/**
+ * Integration tests for the aligner.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public class AlignerIntegrationTest extends WalkerTest {
+    @Test
+    public void testBasicAlignment() {
+        String md5 = "ed098018ffcbd055bee966466044428a";
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-R /humgen/gsa-scr1/GATK_Data/bwa/human_b36_both.fasta" +
+                        " -T Align" +
+                        " -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878_Pilot1_20.trimmed.unmapped.bam" +
+                        " -ob %s",
+                1, // just one output file
+                Arrays.asList(md5));
+        executeTest("testBasicAlignment", spec);
+    }
+}