better way of finding these types of variants

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

@@ -16,10 +16,10 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import htsjdk.variant.variantcontext.{GenotypeType, VariantContext}
-import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
+import htsjdk.variant.variantcontext.{ GenotypeType, VariantContext }
+import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
 import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.utils.{ToolCommand, VcfUtils}
+import nl.lumc.sasc.biopet.utils.{ ToolCommand, VcfUtils }
 
 import scala.collection.JavaConversions._
 import scala.io.Source

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/.
-    * @param genotype genotype
-    * @return boolean
-    */
+   * Check whether genotype is of the from 0/.
+   * @param genotype genotype
+   * @return boolean
+   */
   def isCompoundNoCall(genotype: Genotype): Boolean = {
-    !genotype.isHetNonRef && genotype.isMixed && genotype.getAlleles.last.basesMatch("")
+    genotype.isCalled && genotype.getAlleles.exists(_.isNoCall)
   }
 }