From aee52b85c1c498cba13aa0efaf10340317abbdad Mon Sep 17 00:00:00 2001
From: Kari Stromhaug <kari@fulcrumgenomics.com>
Date: Wed, 30 Mar 2022 09:33:56 -0600
Subject: [PATCH] Remove VariantContext use from VariantMask tool

---
 .../com/fulcrumgenomics/vcf/VariantMask.scala    | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/main/scala/com/fulcrumgenomics/vcf/VariantMask.scala b/src/main/scala/com/fulcrumgenomics/vcf/VariantMask.scala
index 9b5c11846..50c949ef7 100644
--- a/src/main/scala/com/fulcrumgenomics/vcf/VariantMask.scala
+++ b/src/main/scala/com/fulcrumgenomics/vcf/VariantMask.scala
@@ -26,6 +26,7 @@ package com.fulcrumgenomics.vcf
 
 import com.fulcrumgenomics.FgBioDef._
 import com.fulcrumgenomics.fasta.SequenceDictionary
+import com.fulcrumgenomics.vcf.api.{Variant, VcfSource}
 import htsjdk.variant.variantcontext.VariantContext
 import htsjdk.variant.vcf.VCFFileReader
 
@@ -33,18 +34,17 @@ import scala.collection.mutable
 
 object VariantMask {
   /** Generate a variant mask from the provided VCF. */
-  def apply(path: PathToVcf): VariantMask = apply(new VCFFileReader(path.toFile))
+  def apply(path: PathToVcf): VariantMask = apply(VcfSource(path))
 
   /** Generate a variant mask from the provided VCF reader. */
-  def apply(reader: VCFFileReader): VariantMask = {
-    import com.fulcrumgenomics.fasta.Converters.FromSAMSequenceDictionary
-    val dict = reader.getFileHeader.getSequenceDictionary.fromSam
+  def apply(reader: VcfSource): VariantMask = {
+    val dict = reader.header.dict
     require(dict != null && dict.length > 0, "Generating a VariantMask requires VCFs contain contig lines.")
-    apply(reader.iterator(), dict)
+    apply(reader.iterator, dict)
   }
 
   /** Generates a VariantMask from the variants in the provided iterator. */
-  def apply(variants: Iterator[VariantContext], dict: SequenceDictionary) = new VariantMask(variants, dict)
+  def apply(variants: Iterator[Variant], dict: SequenceDictionary) = new VariantMask(variants, dict)
 }
 
 /**
@@ -55,7 +55,7 @@ object VariantMask {
   * @param variants a coordinate sorted iterator of variants
   * @param dict the sequence dictionary for the reference
   */
-class VariantMask(variants: Iterator[VariantContext], val dict: SequenceDictionary) {
+class VariantMask(variants: Iterator[Variant], val dict: SequenceDictionary) {
   private val iterator                    = variants.bufferBetter
   private var currentMask: mutable.BitSet = new mutable.BitSet(0)
   private var currentIndex: Int           = -1
@@ -74,7 +74,7 @@ class VariantMask(variants: Iterator[VariantContext], val dict: SequenceDictiona
     val bits = new mutable.BitSet(ref.length)
     iterator.dropWhile(v => dict(v.getContig).index < refIndex)
       .takeWhile(v => dict(v.getContig).index == refIndex)
-      .filterNot(v => v.isFiltered)
+      .filterNot(v => v.filters.nonEmpty) // TODO verify that this is correct
       .foreach { v =>
         forloop (from=v.getStart, until=v.getEnd+1) { i => bits(i-1) = true }
       }