An integration test based on validating pileup to test parallelism in reads, reference, and RODs. This test runs in less

than a minute and fell over instantly in the case of the Tribble parallelism issue.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3358 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java

@@ -0,0 +1,25 @@
+package org.broadinstitute.sting.gatk.walkers.qc;
+
+import org.junit.Test;
+import org.broadinstitute.sting.WalkerTest;
+
+import java.util.Collections;
+
+/**
+ * Run validating pileup across a set of core data as proof of the integrity of the GATK core.
+ *
+ * @author mhanna
+ * @version 0.1
+ */
+public class ValidatingPileupIntegrationTest extends WalkerTest {
+    @Test
+    public void testEcoliThreaded() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T ValidatingPileup" +
+                " -I /humgen/gsa-scr1/GATK_Data/Validation_Data/MV1994.selected.bam" +
+                " -R /humgen/gsa-scr1/GATK_Data/Validation_Data/Escherichia_coli_K12_MG1655.fasta" +
+                " -B pileup,SAMPileup,/humgen/gsa-scr1/GATK_Data/Validation_Data/MV1994.selected.pileup" +
+                " -S SILENT -nt 8",0, Collections.<String>emptyList());
+        executeTest("testEcoliThreaded",spec);
+    }
+}