feat!: use stronger type claims

rust/Cargo.toml

@@ -12,5 +12,5 @@ chainfile = "0.2.1"
 directories = "5.0"
 
 [dependencies.pyo3]
-version = "0.20.0"
+version = "0.20.2"
 features = ["abi3-py38"]

src/chainlifter/lifter.py

@@ -113,15 +113,30 @@ def convert_coordinate(
         :return: list of coordinate matches (possibly empty)
         """
         try:
-            result = self._chainlifter.lift(chrom, pos, strand)
+            results = self._chainlifter.lift(chrom, pos, strand)
         except _core.NoLiftoverError:
-            result = []
+            results = []
         except _core.ChainfileError:
             _logger.error(
                 "Encountered internal error while converting coordinates - is the chainfile invalid? (%s, %s, %s)",
                 chrom,
                 pos,
                 strand,
             )
-            result = []
-        return result
+            results = []
+        if results:
+            formatted_results = []
+            for result in results:
+                try:
+                    pos = int(result[1])
+                except ValueError:
+                    _logger.error("Got invalid position value in %s", result)
+                    continue
+                try:
+                    strand = Strand(result[2])
+                except ValueError:
+                    _logger.error("Got invalid Strand value in %s", result)
+                    continue
+                formatted_results.append((result[0], pos, strand))
+            results = formatted_results
+        return results

tests/test_liftover.py

@@ -1,5 +1,5 @@
 """Run liftover tests."""
-from chainlifter.lifter import ChainLifter, Genome
+from chainlifter.lifter import ChainLifter, Genome, Strand
 
 
 def test_hg19_to_hg38():
@@ -8,37 +8,37 @@ def test_hg19_to_hg38():
 
     result = ch.convert_coordinate("chr7", 140439611)
     assert len(result) == 1
-    assert result[0] == ["chr7", "140739811", "+"]
+    assert result[0] == ("chr7", 140739811, Strand.POSITIVE)
 
     result = ch.convert_coordinate("chr7", 140439746)
     assert len(result) == 1
-    assert result[0] == ["chr7", "140739946", "+"]
+    assert result[0] == ("chr7", 140739946, Strand.POSITIVE)
 
     result = ch.convert_coordinate("chr7", 140439703)
     assert len(result) == 1
-    assert result[0] == ["chr7", "140739903", "+"]
+    assert result[0] == ("chr7", 140739903, Strand.POSITIVE)
 
     result = ch.convert_coordinate("chr7", 140453136)
     assert len(result) == 1
-    assert result[0] == ["chr7", "140753336", "+"]
+    assert result[0] == ("chr7", 140753336, Strand.POSITIVE)
 
     # coordinate exceeds bounds
     result = ch.convert_coordinate("chr7", 14040053136)
     assert result == []
 
 
 def test_hg38_to_hg19():
-    """Test hg38 to hg19 lifter."""
+    "Test hg38 to hg19 lifter." ""
     ch = ChainLifter(Genome.HG38, Genome.HG19)
 
     result = ch.convert_coordinate("chr7", 140739811)
     assert len(result) == 1
-    assert result[0] == ["chr7", "140439611", "+"]
+    assert result[0] == ("chr7", 140439611, Strand.POSITIVE)
 
     result = ch.convert_coordinate("chr7", 140759820)
     assert len(result) == 1
-    assert result[0] == ["chr7", "140459620", "+"]
+    assert result[0] == ("chr7", 140459620, Strand.POSITIVE)
 
     result = ch.convert_coordinate("chr7", 60878240)
     assert len(result) == 1
-    assert result[0] == ["chr7", "61646115", "+"]
+    assert result[0] == ("chr7", 61646115, Strand.POSITIVE)