Data Processing Pipeline Test

* Added standard pipeline test for the DPP
* Added a full BWA pipeline test for the DPP
* Included the extra files for the reference needed by BWA (to be used by DPP and PPP tests)

public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala

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+package org.broadinstitute.sting.queue.pipeline
+
+/*
+ * Copyright (c) 2011, 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.
+ */
+
+import org.testng.annotations.Test
+import org.broadinstitute.sting.BaseTest
+
+class DataProcessingPipelineTest {
+  @Test
+  def testSimpleBAM {
+    val projectName = "test1"
+    val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
+    val spec = new PipelineTestSpec
+    spec.name = "DataProcessingPipeline"
+    spec.args = Array(
+      " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala",
+      " -R " + BaseTest.testDir + "exampleFASTA.fasta",
+      " -i " + BaseTest.testDir + "exampleBAM.bam",
+      " -D " + BaseTest.testDir + "exampleDBSNP.vcf",
+      " -nv ",
+      " -p " + projectName).mkString
+    spec.fileMD5s += testOut -> "69ba216bcf1e2dd9b6bd631ef99efda9"
+    PipelineTest.executeTest(spec)
+  }
+
+  @Test
+  def testBWAPEBAM {
+    val projectName = "test2"
+    val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
+    val spec = new PipelineTestSpec
+    spec.name = "DataProcessingPipeline"
+    spec.args = Array(
+      " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala",
+      " -R " + BaseTest.testDir + "exampleFASTA.fasta",
+      " -i " + BaseTest.testDir + "exampleBAM.bam",
+      " -D " + BaseTest.testDir + "exampleDBSNP.vcf",
+      " -nv ",
+      " -bwa /home/unix/carneiro/bin/bwa",
+      " -bwape ",
+      " -p " + projectName).mkString
+    spec.fileMD5s += testOut -> "3134cbeae1561ff8e6b559241f9ed7f5"
+    PipelineTest.executeTest(spec)
+  }
+
+}

public/testdata/exampleFASTA.fasta.amb

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+100000 1 0

public/testdata/exampleFASTA.fasta.ann

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+100000 1 11
+0 chr1 (null)
+0 100000 0