fix: close fh and remove obsolete comment

fulcrumgenomics · Jan 16, 2025 · 8512844 · 8512844
1 parent c69320f
commit 8512844
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Showing 2 changed files with 2 additions and 9 deletions.
diff --git a/fgpyo/fasta/sequence_dictionary.py b/fgpyo/fasta/sequence_dictionary.py
@@ -498,13 +498,6 @@ def from_sam(
 
         return seq_dict
 
-    # TODO: mypy doesn't like these
-    # @overload
-    # def __getitem__(self, key: str) -> SequenceMetadata: ...
-    #
-    # @overload
-    # def __getitem__(self, index: int) -> SequenceMetadata: ...
-
     def __getitem__(self, key: Union[str, int]) -> SequenceMetadata:
         return self._dict[key] if isinstance(key, str) else self.infos[key]
 

diff --git a/tests/fgpyo/fasta/test_sequence_dictionary.py b/tests/fgpyo/fasta/test_sequence_dictionary.py
@@ -333,9 +333,9 @@ def test_sequence_dictionary_to_and_from_sam() -> None:
         header_dict={"HD": {"VN": "1.5"}, "SQ": mapping, "RG": [{"ID": "foo"}]}
     )
     samfile: Path = builder.SamBuilder(sd=mapping).to_path()
-    alignment: pysam.AlignmentFile = reader(samfile)
+    with reader(samfile) as alignment_fh:  # pysam.AlignmentFile
+        assert SequenceDictionary.from_sam(alignment_fh) == sd
     assert SequenceDictionary.from_sam(samfile) == sd
-    assert SequenceDictionary.from_sam(alignment) == sd
     assert SequenceDictionary.from_sam(mapping) == sd
     assert SequenceDictionary.from_sam(header) == sd
     assert sd.to_sam_header(extra_header={"RG": [{"ID": "foo"}]})