Added unit test for bammetrics

public/bammetrics/pom.xml

@@ -39,5 +39,17 @@
             <artifactId>BiopetFramework</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.11</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 </project>

public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

+package nl.lumc.sasc.biopet.pipelines.bammetrics
+
+import java.io.File
+
+import com.google.common.io.Files
+import nl.lumc.sasc.biopet.core.config.Config
+import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
+import nl.lumc.sasc.biopet.extensions.picard._
+import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
+import nl.lumc.sasc.biopet.scripts.CoverageStats
+import nl.lumc.sasc.biopet.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.apache.commons.io.FileUtils
+import org.broadinstitute.gatk.queue.QSettings
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.{ Test, DataProvider, AfterClass }
+
+/**
+ * Created by pjvan_thof on 4/30/15.
+ */
+class BamMetricsTest extends TestNGSuite with Matchers {
+
+  def initPipeline(map: Map[String, Any]): BamMetrics = {
+    new BamMetrics() {
+      override def configName = "bammetrics"
+      override def globalConfig = new Config(map)
+      qSettings = new QSettings
+      qSettings.runName = "test"
+    }
+  }
+
+  @DataProvider(name = "bammetricsOptions")
+  def bammetricsOptions = {
+    val rois = Array(0, 1, 2, 3)
+    val amplicon = Array(true, false)
+    val rna = Array(true, false)
+
+    for (
+      rois <- rois;
+      amplicon <- amplicon;
+      rna <- rna
+    ) yield Array(rois, amplicon, rna)
+  }
+
+  @Test(dataProvider = "bammetricsOptions")
+  def testFlexiprep(rois: Int, amplicon: Boolean, rna: Boolean) = {
+    val map = ConfigUtils.mergeMaps(Map("output_dir" -> BamMetricsTest.outputDir, "rna_metrcis" -> rna
+    ), Map(BamMetricsTest.executables.toSeq: _*)) ++
+      (if (amplicon) Map("amplicon_bed" -> "amplicon.bed") else Map()) ++
+      Map("regions_of_interest" -> (1 to rois).map("roi_" + _ + ".bed").toList)
+    val bammetrics: BamMetrics = initPipeline(map)
+
+    bammetrics.inputBam = new File("input.bam")
+    bammetrics.sampleId = Some("1")
+    bammetrics.libId = Some("1")
+    bammetrics.script()
+
+    var regions: Int = rois + (if (amplicon) 1 else 0)
+
+    bammetrics.functions.count(_.isInstanceOf[CollectRnaSeqMetrics]) shouldBe (if (rna) 1 else 0)
+    bammetrics.functions.count(_.isInstanceOf[CollectWgsMetrics]) shouldBe 1
+    bammetrics.functions.count(_.isInstanceOf[CollectMultipleMetrics]) shouldBe 1
+    bammetrics.functions.count(_.isInstanceOf[CalculateHsMetrics]) shouldBe (if (amplicon) 1 else 0)
+    bammetrics.functions.count(_.isInstanceOf[CollectTargetedPcrMetrics]) shouldBe (if (amplicon) 1 else 0)
+    bammetrics.functions.count(_.isInstanceOf[BiopetFlagstat]) shouldBe (1 + (regions * 2))
+    bammetrics.functions.count(_.isInstanceOf[SamtoolsFlagstat]) shouldBe (1 + (regions * 2))
+    bammetrics.functions.count(_.isInstanceOf[BedtoolsIntersect]) shouldBe (regions * 2)
+
+    bammetrics.functions.count(_.isInstanceOf[BedtoolsCoverage]) shouldBe regions
+    bammetrics.functions.count(_.isInstanceOf[CoverageStats]) shouldBe regions
+  }
+
+  // remove temporary run directory all tests in the class have been run
+  @AfterClass
+  def removeTempOutputDir() = {
+    FileUtils.deleteDirectory(BamMetricsTest.outputDir)
+  }
+}
+
+object BamMetricsTest {
+  val outputDir = Files.createTempDir()
+
+  val executables = Map(
+    "refFlat" -> "bla.refFlat",
+    "reference" -> "reference.fa",
+    "samtools" -> Map("exe" -> "test"),
+    "bedtools" -> Map("exe" -> "test")
+  )
+}