Added unit test to SnptestToVcf

public/biopet-tools/src/test/resources/test.empty.snptest

+# Completed successfully at 2016-04-08 13:47:05

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

+# Analysis: "snptest"
+#  started: 2016-04-08 13:44:20
+#
+# Analysis properties:
+#   -analysis_name snptest (user-supplied)
+#   -data /exports/sasc/project-171/analysis/snptest/18/18-22307785-33461676.vcf.gz /exports/sasc/project-171/src/Phenotypes_knee_hip_hand.fixed2.txt (user-supplied)
+#   -o /exports/sasc/project-171/analysis/snptest/18/18-22307785-33461676.snptest (user-supplied)
+#   -summary_stats_only  (user-supplied)
+#
+alternate_ids rsid chromosome position alleleA alleleB index average_maximum_posterior_call info cohort_1_AA cohort_1_AB cohort_1_BB cohort_1_NULL all_AA all_AB all_BB all_NULL all_total all_maf missing_data_proportion comment
+rs184556815 rs184556815 18 22307810 G T 1 1 1 2869 0 0 0 2869 0 0 0 2869 0 0 NA
+rs143248971 rs143248971 18 22307875 C T 2 1 1 2869 0 0 0 2869 0 0 0 2869 0 0 NA
+rs74666159 rs74666159 18 22307884 C T 3 1 1 2690 177 2 0 2690 177 2 0 2869 0.0315441 0 NA
+# Completed successfully at 2016-04-08 13:47:05

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

@@ -45,6 +45,4 @@ object GensToVcfTest {
   private def resourcePath(p: String): String = {
     Paths.get(getClass.getResource(p).toURI).toString
   }
-
-
 }

public/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/SnptestToVcfTest.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 SnptestToVcfTest extends TestNGSuite with Matchers {
+  @Test
+  def testSnptest: Unit = {
+    val output = File.createTempFile("test.", ".vcf.gz")
+    output.deleteOnExit()
+    SnptestToVcf.main(Array(
+      "--inputInfo", SnptestToVcfTest.resourcePath("/test.snptest"),
+      "--outputVcf", output.getAbsolutePath,
+      "--referenceFasta", SnptestToVcfTest.resourcePath("/fake_chrQ.fa"),
+      "--contig", "chrQ"
+    ))
+  }
+
+  @Test
+  def testEmptySnptest: Unit = {
+    val output = File.createTempFile("test.", ".vcf.gz")
+    output.deleteOnExit()
+    SnptestToVcf.main(Array(
+      "--inputInfo", SnptestToVcfTest.resourcePath("/test.empty.snptest"),
+      "--outputVcf", output.getAbsolutePath,
+      "--referenceFasta", SnptestToVcfTest.resourcePath("/fake_chrQ.fa"),
+      "--contig", "chrQ"
+    ))
+  }
+}
+
+object SnptestToVcfTest {
+  private def resourcePath(p: String): String = {
+    Paths.get(getClass.getResource(p).toURI).toString
+  }
+}