Added spec parsing unit test

public/gwas-test/src/test/resources/specs/files.specs

+{
+        files = (
+                {
+                        chromosome = "chrQ";
+                        name = "imputation_06/test";
+                        orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr1";
+                },
+                {
+                        chromosome = "chrQ";
+                        name = "imputation_06/test";
+                        orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr1";
+                },
+                {
+                        chromosome = "chrQ";
+                        name = "imputation_06/test";
+                        orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr22";
+                },
+                {
+                        chromosome = "chrQ";
+                        name = "imputation_06/test";
+                        orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr22";
+                }
+        );
+        jids = ( "2102064" );
+        type = "tped3col";
+}
\ No newline at end of file

public/gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala

@@ -32,6 +32,35 @@ class GwasTestTest extends TestNGSuite with Matchers {
     pipeline.script()
   }
 
+  @Test
+  def testFromGens: Unit = {
+    val pipeline = initPipeline(GwasTestTest.config ++
+      Map("input_gens" -> List(Map("genotypes" -> GwasTestTest.vcfFile, "contig" -> "chrQ"))
+      )
+    )
+    pipeline.script()
+  }
+
+  @Test
+  def testWrongContig: Unit = {
+    val pipeline = initPipeline(GwasTestTest.config ++
+      Map("input_gens" -> List(Map("genotypes" -> GwasTestTest.vcfFile, "contig" -> "chrBla"))
+      )
+    )
+    intercept[IllegalStateException] {
+      pipeline.script()
+    }
+  }
+
+  @Test
+  def testFromSpecs: Unit = {
+    val pipeline = initPipeline(GwasTestTest.config ++
+      Map("imute_specs_file" -> GwasTestTest.resourcePath("/specs/files.specs"))
+    )
+    pipeline.script()
+  }
+
+
   @Test
   def testEmpty: Unit = {
     val pipeline = initPipeline(GwasTestTest.config)