[AVOCADO-247] Don't apply max AF filter to hetalts.

Resolves #247.
bigdatagenomics · Jun 4, 2017 · 664ee45 · 664ee45
1 parent c3e48f5
commit 664ee45
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diff --git a/avocado-core/src/main/scala/org/bdgenomics/avocado/util/HardFilterGenotypes.scala b/avocado-core/src/main/scala/org/bdgenomics/avocado/util/HardFilterGenotypes.scala
@@ -541,7 +541,10 @@ private[avocado] object HardFilterGenotypes extends Serializable {
   private[util] def hardFilterMaxAllelicFraction(genotype: Genotype,
                                                  maxAlleleFraction: Float,
                                                  msg: String): Option[String] = {
-    val gtIsHom = genotype.getAlleles.forall(_ == GenotypeAllele.ALT)
+    // treat het-alt as hom
+    val gtIsHom = genotype.getAlleles.forall(ga => {
+      ga == GenotypeAllele.ALT || ga == GenotypeAllele.OTHER_ALT
+    })
     if (gtIsHom) {
       None
     } else {

diff --git a/avocado-core/src/test/scala/org/bdgenomics/avocado/util/HardFilterGenotypesSuite.scala b/avocado-core/src/test/scala/org/bdgenomics/avocado/util/HardFilterGenotypesSuite.scala
@@ -61,6 +61,11 @@ class HardFilterGenotypesSuite extends AvocadoFunSuite {
       .setAlleles(Seq(GenotypeAllele.ALT, GenotypeAllele.ALT))
   }
 
+  def hetAlt: Genotype.Builder = {
+    Genotype.newBuilder
+      .setAlleles(Seq(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT))
+  }
+
   def altWithAnn: Genotype.Builder = {
     alt
       .setVariantCallingAnnotations(VariantCallingAnnotations.newBuilder
@@ -405,5 +410,11 @@ class HardFilterGenotypesSuite extends AvocadoFunSuite {
       .setAlternateReadDepth(45)
       .build, 0.666f, "MAXAF")
     assert(hom.isEmpty)
+
+    val het = HardFilterGenotypes.hardFilterMaxAllelicFraction(hetAlt.setGenotypeQuality(50)
+      .setReadDepth(50)
+      .setAlternateReadDepth(40)
+      .build, 0.666f, "MAXAF")
+    assert(het.isEmpty)
   }
 }