attempt fix for #386

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
+import nl.lumc.sasc.biopet.utils.{ToolCommand, VcfUtils}
 
 import scala.collection.JavaConversions._
 import scala.io.Source
@@ -315,11 +315,11 @@ object VcfFilter extends ToolCommand {
    * Checks if given samples does have a variant hin this record
    *
    * @param record VCF record
-   * @param mustHaveVariant List of samples that should have this variant
+   * @param samples List of samples that should have this variant
    * @return true if filter passed
    */
-  def mustHaveVariant(record: VariantContext, mustHaveVariant: List[String]): Boolean = {
-    !mustHaveVariant.map(record.getGenotype).exists(a => a.isHomRef || a.isNoCall)
+  def mustHaveVariant(record: VariantContext, samples: List[String]): Boolean = {
+    !samples.map(record.getGenotype).exists(a => a.isHomRef || a.isNoCall || VcfUtils.isCompoundNoCall(a))
   }
 
   /** Checks if given samples have the same genotype */

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

@@ -140,4 +140,13 @@ object VcfUtils {
     reader.close()
     !hasNext
   }
+
+  /**
+    * 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("")
+  }
 }