Allow the OverlapDetector to be generic over input feature types

pybedlite/overlap_detector.py

@@ -225,7 +225,7 @@ def __iter__(self) -> Iterator[_GenericGenomicSpan]:
         return itertools.chain(*self._refname_to_intervals.values())
 
     @staticmethod
-    def _reference_name(interval: GenomicSpan) -> str:
+    def _reference_sequence_name(interval: GenomicSpan) -> str:
         """Return the reference name of a given interval."""
         if isinstance(interval, Interval) or hasattr(interval, "refname"):
             return interval.refname
@@ -264,7 +264,7 @@ def add(self, interval: _GenericGenomicSpan) -> None:
         if not isinstance(interval, Hashable):
             raise ValueError(f"Interval feature is not hashable but should be: {interval}")
 
-        refname = self._reference_name(interval)
+        refname = self._reference_sequence_name(interval)
         if refname not in self._refname_to_tree:
             self._refname_to_tree[refname] = cr.cgranges()  # type: ignore
             self._refname_to_indexed[refname] = False
@@ -302,7 +302,7 @@ def overlaps_any(self, interval: GenomicSpan) -> bool:
             True if and only if the given interval overlaps with any interval in this
             detector.
         """
-        refname = self._reference_name(interval)
+        refname = self._reference_sequence_name(interval)
         tree = self._refname_to_tree.get(refname)
         if tree is None:
             return False
@@ -326,7 +326,7 @@ def get_overlaps(self, interval: GenomicSpan) -> List[_GenericGenomicSpan]:
             The list of intervals in this detector that overlap the given interval, or the empty
             list if no overlaps exist.  The intervals will be return in ascending genomic order.
         """
-        refname = self._reference_name(interval)
+        refname = self._reference_sequence_name(interval)
         tree = self._refname_to_tree.get(refname)
         if tree is None:
             return []
@@ -345,7 +345,7 @@ def get_overlaps(self, interval: GenomicSpan) -> List[_GenericGenomicSpan]:
                     intv.start,
                     intv.end,
                     self._is_negative(intv),
-                    self._reference_name(intv),
+                    self._reference_sequence_name(intv),
                 ),
             )