Adding tests for VcfToTsv

public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala

+package nl.lumc.sasc.biopet.tools
+
+import java.nio.file.Paths
+import java.util
+import scala.collection.JavaConversions._
+
+import org.scalatest.Matchers
+import org.scalatest.mock.MockitoSugar
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.util.Random
+
+/**
+ * Created by ahbbollen on 13-4-15.
+ */
+class VcfToTsvTest extends TestNGSuite with MockitoSugar with Matchers {
+  import VcfToTsv._
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+  val rand = new Random()
+
+  val vepped = resourcePath("/VEP_oneline.vcf")
+  val unvepped = resourcePath("/unvepped.vcf")
+
+  @Test def testAllFields() = {
+    val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+    val arguments = Array("-I", unvepped, "-o", tmp_path, "--all_info")
+    main(arguments)
+  }
+
+  @Test def testSpecificField() = {
+    val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+    val arguments = Array("-I", vepped, "-o", tmp_path, "-i", "CSQ")
+    main(arguments)
+  }
+
+  @Test def testNewSeparators() = {
+    val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+    val arguments = Array("-I", vepped, "-o", tmp_path, "--all_info", "--separator", ",", "--list_separator", "|")
+    main(arguments)
+  }
+
+  @Test(expectedExceptions = Array(classOf[IllegalArgumentException]))
+  def testIdenticalSeparators() = {
+    val tmp_path = "/tmp/VcfToTsv_" + rand.nextString(10) + ".tsv"
+    val arguments = Array("-I", vepped, "-o", tmp_path, "--all_info", "--separator", ",")
+    main(arguments)
+  }
+
+  @Test def testFormatter() = {
+    val formatter = createFormatter(2)
+    formatter.format(5000.12345) should be("5000.12")
+    val nformatter = createFormatter(3)
+    nformatter.format(5000.12345) should be("5000.123")
+  }
+
+  @Test def testSortFields() = {
+    val unsortedFields = Set("Child01-GT", "Mother02-GT", "Father03-GT", "INFO-Something", "INFO-ScoreSomething",
+      "INFO-AlleleScoreSomething", "WeirdField")
+    val samples = List("Child01", "Father03", "Mother02")
+
+    val sorted = sortFields(unsortedFields, samples)
+    sorted should be(List("WeirdField", "INFO-AlleleScoreSomething", "INFO-ScoreSomething", "INFO-Something",
+    "Child01-GT", "Father03-GT", "Mother02-GT"))
+  }
+
+}