VcfFilter addition for musthavegenotypes. See #186.

Ended up using HTSJDK nomenclature for genotype types
I.e: HET, HOM_REF, HOM_VAR, MIXED, NO_CALL and UNAVAILABLE

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import htsjdk.variant.variantcontext.VariantContext
+import htsjdk.variant.variantcontext.{ GenotypeType, VariantContext }
 import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
 import htsjdk.variant.vcf.VCFFileReader
 import nl.lumc.sasc.biopet.core.config.Configurable
@@ -72,6 +72,7 @@ object VcfFilter extends ToolCommand {
                   minSamplesPass: Int = 1,
                   mustHaveVariant: List[String] = Nil,
                   calledIn: List[String] = Nil,
+                  mustHaveGenotype: List[String] = Nil,
                   deNovoInSample: String = null,
                   resToDom: List[Trio] = Nil,
                   trioCompound: List[Trio] = Nil,
@@ -126,6 +127,10 @@ object VcfFilter extends ToolCommand {
     opt[String]("calledIn") unbounded () valueName "<sample>" action { (x, c) =>
       c.copy(calledIn = x :: c.calledIn)
     } text "Must be called in this sample"
+    opt[String]("mustHaveGenotype") unbounded () valueName "<sample:genotype>" action { (x, c) =>
+      c.copy(mustHaveGenotype = x :: c.mustHaveGenotype)
+    } validate { x => if (x.split(":").length == 2 && Set("HET", "HOM_REF", "HOM_VAR", "MIXED", "NO_CALL", "UNAVAILABLE").contains(x.split(":")(1))) success else failure("--mustHaveGenotype should be in this format: sample:genotype")
+    } text "Must have genotoype <genotype> for this sample. Genotype can be HET, HOM_REF, HOM_VAR, MIXED, NO_CALL and UNAVAILABLE"
     opt[String]("diffGenotype") unbounded () valueName "<sample:sample>" action { (x, c) =>
       c.copy(diffGenotype = (x.split(":")(0), x.split(":")(1)) :: c.diffGenotype)
     } validate { x => if (x.split(":").length == 2) success else failure("--notSameGenotype should be in this format: sample:sample")
@@ -183,7 +188,7 @@ object VcfFilter extends ToolCommand {
         hasMinSampleDepth(record, cmdArgs.minSampleDepth, cmdArgs.minSamplesPass) &&
         minAlternateDepth(record, cmdArgs.minAlternateDepth, cmdArgs.minSamplesPass) &&
         (cmdArgs.mustHaveVariant.isEmpty || mustHaveVariant(record, cmdArgs.mustHaveVariant)) &&
-        calledIn(record, cmdArgs.calledIn) &&
+        calledIn(record, cmdArgs.calledIn) && hasGenotype(record, cmdArgs.mustHaveGenotype) &&
         (cmdArgs.diffGenotype.isEmpty || cmdArgs.diffGenotype.forall(x => notSameGenotype(record, x._1, x._2))) &&
         (
           cmdArgs.filterHetVarToHomVar.isEmpty ||
@@ -220,6 +225,17 @@ object VcfFilter extends ToolCommand {
     else true
   }
 
+  /**
+   * Checks if given genotypes for given samples are there
+   * @param record VCF record
+   * @param samplesGenotypes samples and their associated genotypes to be checked (of format sample:genotype)
+   * @return false when filter fails
+   */
+  def hasGenotype(record: VariantContext, samplesGenotypes: List[String]): Boolean = {
+    if (!samplesGenotypes.forall(x => record.getGenotype(x.split(":")(0)).getType == GenotypeType.valueOf(x.split(":")(1)))) false
+    else true
+  }
+
   /**
    * Checks if record has atleast minQualScore
    * @param record VCF record