extra safeguards. potential genotype 1/. is still a call.

 Tests in VcfUtils

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala

@@ -142,11 +142,11 @@ object VcfUtils {
   }
 
   /**
-   * Check whether genotype is of the from 0/.
+   * Check whether genotype is of the form 0/.
    * @param genotype genotype
    * @return boolean
    */
   def isCompoundNoCall(genotype: Genotype): Boolean = {
-    genotype.isCalled && genotype.getAlleles.exists(_.isNoCall)
+    genotype.isCalled && genotype.getAlleles.exists(_.isNoCall) && genotype.getAlleles.exists(_.isReference)
   }
 }

biopet-utils/src/test/scala/VcfUtilsTest.scala

+import htsjdk.variant.variantcontext.{Allele, Genotype, GenotypeBuilder}
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.collection.JavaConversions._
+
+import nl.lumc.sasc.biopet.utils.VcfUtils
+
+/**
+  * Created by Sander Bollen on 4-10-16.
+  */
+class VcfUtilsTest extends TestNGSuite with Matchers {
+
+  @Test
+  def testCompoundNoCall(): Unit = {
+    val noAllele = Allele.NO_CALL
+    val refAllele = Allele.create("A", true)
+    val compoundNoCall = GenotypeBuilder.create("sample_01", List(noAllele, refAllele))
+    VcfUtils.isCompoundNoCall(compoundNoCall) shouldBe true
+
+    val altAllele = Allele.create("G", false)
+    val normalGenotype = GenotypeBuilder.create("sample_01", List(refAllele, altAllele))
+    VcfUtils.isCompoundNoCall(normalGenotype) shouldBe false
+
+    val completeNoCall = GenotypeBuilder.create("sample_01", List(noAllele, noAllele))
+    VcfUtils.isCompoundNoCall(completeNoCall) shouldBe false
+  }
+
+}