Added filter on HET_REF

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/VcfFilter.scala

@@ -22,6 +22,7 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
   var minTotalDepth: Option[Int] = _
   var minAlternateDepth: Option[Int] = _
   var minSamplesPass: Option[Int] = _
+  var filterRefCalls: Boolean = _
   
   override val defaultVmem = "8G"
   memoryLimit = Option(4.0)
@@ -31,6 +32,7 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
     minTotalDepth = config("min_total_depth")
     minAlternateDepth = config("min_alternate_depth")
     minSamplesPass = config("min_samples_pass")
+    filterRefCalls = config("filter_ref_calls")
   }
   
   override def commandLine = super.commandLine + 
@@ -39,7 +41,8 @@ class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
     optional("-minSampleDepth", minSampleDepth) +
     optional("-minTotalDepth", minTotalDepth) +
     optional("-minAlternateDepth", minAlternateDepth) + 
-    optional("-minSamplesPass", minSamplesPass)
+    optional("-minSamplesPass", minSamplesPass) +
+    conditional(filterRefCalls, "-filterRefCalls")
 }
 
 object VcfFilter {
@@ -49,6 +52,7 @@ object VcfFilter {
   var minTotalDepth = -1
   var minAlternateDepth = -1
   var minSamplesPass = 0
+  var filterRefCalls = false
   /**
    * @param args the command line arguments
    */
@@ -61,6 +65,7 @@ object VcfFilter {
         case "-minTotalDepth" => minTotalDepth = args(t+1).toInt
         case "-minAlternateDepth" => minAlternateDepth = args(t+1).toInt
         case "-minSamplesPass" => minSamplesPass = args(t+1).toInt
+        case "-filterRefCalls" => filterRefCalls = true
         case _ =>
       }
     }
@@ -73,7 +78,8 @@ object VcfFilter {
     for (record <- reader) {
       val genotypes = for (genotype <- record.getGenotypes) yield {
         genotype.getDP >= minSampleDepth && 
-        List(genotype.getAD:_*).tail.count(_ >= minAlternateDepth) > 0
+        List(genotype.getAD:_*).tail.count(_ >= minAlternateDepth) > 0 &&
+        !(filterRefCalls && genotype.isHomRef)
       }
       
       if (record.getAttributeAsInt("DP", -1) >= minTotalDepth && genotypes.count(_ == true) >= minSamplesPass)