Added test

bam2wig/pom.xml

@@ -45,6 +45,18 @@
             <artifactId>BiopetExtensions</artifactId>
             <version>${project.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest_2.10</artifactId>
+            <version>2.2.1</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
 </project>
\ No newline at end of file

bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala

+package nl.lumc.sasc.biopet.pipelines.bamtobigwig
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+
+/**
+  * Created by pjvanthof on 09/05/16.
+  */
+class BamToChromSizesTest extends TestNGSuite with Matchers {
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  @Test
+  def testChromSizes: Unit = {
+    val bamFile = new File(resourcePath("/empty.bam"))
+    val bamToChromSizes = new BamToChromSizes(null)
+    bamToChromSizes.bamFile = bamFile
+    bamToChromSizes.chromSizesFile = File.createTempFile("chrom.", ".sizes")
+    bamToChromSizes.chromSizesFile.deleteOnExit()
+    bamToChromSizes.run()
+    Source.fromFile(bamToChromSizes.chromSizesFile).getLines().toList shouldBe List("chrQ\t10000", "chrR\t10000")
+  }
+}