Merge branch 'fix-biopet-509' into 'develop'

Check whether sample exists in vcf file [Biopet-509]



See merge request !506

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala

@@ -319,6 +319,11 @@ object VcfFilter extends ToolCommand {
    * @return true if filter passed
    */
   def mustHaveVariant(record: VariantContext, samples: List[String]): Boolean = {
+    samples.foreach { s =>
+      if (!record.getSampleNames.toList.contains(s)) {
+        throw new IllegalArgumentException(s"Sample name $s does not exist in VCF file")
+      }
+    }
     !samples.map(record.getGenotype).exists(a => a.isHomRef || a.isNoCall || VcfUtils.isCompoundNoCall(a))
   }
 

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala

@@ -186,6 +186,8 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers {
     mustHaveVariant(record, List("Sample_101", "Sample_102")) shouldBe true
     mustHaveVariant(record, List("Sample_101", "Sample_102", "Sample_103")) shouldBe false
 
+    an[IllegalArgumentException] shouldBe thrownBy(mustHaveVariant(record, List("notExistant")))
+
     val starReader = new VCFFileReader(star, false)
     starReader.iterator().foreach(x => mustHaveVariant(x, List("Sample_101")) shouldBe false)
   }