broadinstitute · lbergelson · Feb 8, 2019 · Jan 14, 2018 · Feb 8, 2019
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/ContextShard.java b/src/main/java/org/broadinstitute/hellbender/engine/ContextShard.java
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSpark.java b/src/main/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSpark.java
diff --git a/...n/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSparkOptimized.java b/...n/java/org/broadinstitute/hellbender/engine/spark/AddContextDataToReadSparkOptimized.java
diff --git a/src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSource.java b/src/main/java/org/broadinstitute/hellbender/engine/spark/datasources/ReadsSparkSource.java
@@ -198,7 +198,7 @@ static String checkCramReference(final JavaSparkContext ctx, final String filePa
      * Tests if a given SAMRecord overlaps any interval in a collection. This is only used as a fallback option for
      * formats that don't support query-by-interval natively at the Hadoop-BAM layer.
      */
-    //TODO: use IntervalsSkipList, see https://github.com/broadinstitute/gatk/issues/1531
+    //TODO: use OverlapDetector, see https://github.com/broadinstitute/gatk/issues/1531
     private static boolean samRecordOverlaps(final SAMRecord record, final TraversalParameters traversalParameters ) {
         if (traversalParameters == null) {
             return true;

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/collections/IntervalsSkipList.java b/src/main/java/org/broadinstitute/hellbender/utils/collections/IntervalsSkipList.java
diff --git a/...main/java/org/broadinstitute/hellbender/utils/collections/IntervalsSkipListOneContig.java b/...main/java/org/broadinstitute/hellbender/utils/collections/IntervalsSkipListOneContig.java