Fix a bug in Cigar class

Author: Kari Stromhaug

src/main/scala/com/fulcrumgenomics/vcf/AssessPhasing.scala

@@ -649,7 +649,7 @@ private[vcf] object PhaseCigar {
             assumeFixedAlleleOrder: Boolean = false): PhaseCigar = {
     val iter = pairedIterator.filter {
       // ensure the alleles are the same when both truth and call are called
-      case ((Some(t: VCtx), Some(c: VCtx))) =>
+      case (Some(t: VCtx), Some(c: VCtx)) =>
         !skipMismatchingAlleles || t.alleles.toSet == c.alleles.toSet
       case _ => true
     }.flatMap { case (t, c) => // collect metrics but only keep sites where either variant (i.e. truth or call) is phased.
@@ -793,8 +793,8 @@ private[vcf] object PhaseCigar {
     * [[Mismatch]] otherwise.
     */
   private[vcf] def cigarTypeForVariantContexts(truth: Variant, call: Variant): PhaseCigarOp = {
-    val truthAlleles  = truth.gts.next().alleles.toSeq
-    val calledAlleles = call.gts.next().alleles.toSeq
+    val truthAlleles  = truth.gts.next().calls.toSeq
+    val calledAlleles = call.gts.next().calls.toSeq
     require(truthAlleles.length == calledAlleles.length)
     require(truthAlleles.length == 2)
     if (truthAlleles.head != calledAlleles.head || truthAlleles.last != calledAlleles.last) PhaseCigarOp.Mismatch