fix(htsget): overlap behavior for enclosed regions (#212)

* chore(dep): drop unused calamus

* chore(dep): constrain minimal compatible linkml version

* sec(dep): floor pynacl>=1.6.2 to protect from CVE-2025-69277

* chore(dep): declare explicit imports

* chore(dep): cap typer for sphinx-click compat

* docs(cli): fix out of date cli path

* chore(dep): update lock file

* test(c4gh): adapt to new key-generation api

* chore(c4gh): drop unnecessary comment

* test: add check for preserved links post-removal

* fix(api): preserve links upon remove

* test(htsget): add overlap test for fully contained region

* fix(htsget): consider contained interval as overlap

Author: cmdoret

src/modos/genomics/region.py

@@ -131,14 +131,13 @@ def from_pysam(
                 raise ValueError("Record must have coordinates")
 
     def overlaps(self, other: Region) -> bool:
-        """Checks if other in self.
-        This check if any portion of other overlaps with self.
+        """Checks if any portion of other overlaps with self.
+
+        Uses half-open interval semantics, so adjacent regions
+        (e.g. [10, 20) and [20, 30)) do not overlap.
         """
         same_chrom = self.chrom == other.chrom
-        starts_in = self.start <= other.start <= self.end
-        ends_in = self.start <= other.end <= self.end
-
-        return same_chrom and (starts_in or ends_in)
+        return same_chrom and self.start < other.end and other.start < self.end
 
     def contains(self, other: Region) -> bool:
         """Checks if other is fully contained in self."""

tests/test_region.py

@@ -22,6 +22,14 @@ def test_overlap():
     assert not region3.overlaps(region1)
 
 
+def test_overlap_contained_region():
+    """A region fully contained in another overlaps it, both ways."""
+    outer = Region(chrom="chr1", start=10, end=100)
+    inner = Region(chrom="chr1", start=40, end=50)
+    assert outer.overlaps(inner)
+    assert inner.overlaps(outer)
+
+
 def test_contain():
     region1 = Region(chrom="chr1", start=10, end=20)
     region2 = Region(chrom="chr1", start=15, end=18)