Adding test to GensToVcf

public/biopet-tools/src/test/resources/gens.samples

+ID_1	ID_2	missing	hip	knee	hand	knee_or_hip	sex	age	bmi
+0 0 0 D D D D D P P
+sample-1	fam-1	0.0	2	NA	2	2	1	59.0767123287671	27.1314117909924
+sample-2	fam-1	0.0	2	NA	NA	2	2	48.4958904109589	23.8754325259516
+sample-3	fam-1	0.0	NA	NA	NA	NA	2	57.0876712328767	45.8842609074008

public/biopet-tools/src/test/resources/test.gens

+--- rs1 30 A C 1 0 0 0 1 0 0 0 1
+--- rs2 40 A - 1 0 0 0 1 0 0 0 1
+--- rs3 50 A AT 1 0 0 0 1 0 0 0 1
\ No newline at end of file

public/biopet-tools/src/test/resources/test.gens_info

+snp_id rs_id position exp_freq_a1 info certainty type info_type0 concord_type0 r2_type0
+--- rs1 30 0.037 0.535 0.958 0 -1 -1 -1
+--- rs2 40 0.023 0.621 0.978 0 -1 -1 -1
+--- rs3 50 0.000 0.114 0.999 0 -1 -1 -1

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

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+  * Created by pjvan_thof on 4/11/16.
+  */
+class GensToVcfTest extends TestNGSuite with Matchers {
+  @Test
+  def testGensOnly: Unit = {
+    val output = File.createTempFile("test.", ".vcf.gz")
+    GensToVcf.main(Array(
+      "--inputGenotypes", GensToVcfTest.resourcePath("/test.gens"),
+      "--outputVcf", output.getAbsolutePath,
+      "--referenceFasta", GensToVcfTest.resourcePath("/fake_chrQ.fa"),
+      "--contig", "chrQ",
+      "--samplesFile", GensToVcfTest.resourcePath("/gens.samples")
+    ))
+  }
+
+  @Test
+  def testGensInfo: Unit = {
+    val output = File.createTempFile("test.", ".vcf.gz")
+    GensToVcf.main(Array(
+      "--inputGenotypes", GensToVcfTest.resourcePath("/test.gens"),
+      "--inputInfo", GensToVcfTest.resourcePath("/test.gens_info"),
+      "--outputVcf", output.getAbsolutePath,
+      "--referenceFasta", GensToVcfTest.resourcePath("/fake_chrQ.fa"),
+      "--contig", "chrQ",
+      "--samplesFile", GensToVcfTest.resourcePath("/gens.samples"),
+      "--sortInput"
+    ))
+  }
+
+}
+
+object GensToVcfTest {
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+
+
+}