refactor: PR changes

fgpyo/io/__init__.py

@@ -267,35 +267,36 @@ def suppress_stderr() -> Generator[None, None, None]:
 
 def assert_fasta_is_indexed(
     fasta: Path,
-    faidx: bool = True,
-    dictionary: bool = True,
-    bwa: bool = True,
+    /,
+    dictionary: bool = False,
+    bwa: bool = False,
 ) -> None:
     """
     Verify that a FASTA is readable and has the expected index files.
 
+    The existence of the FASTA index generated by `samtools faidx` will always be verified. The
+    existence of the index files generated by `samtools dict` and `bwa index` may be optionally
+    verified.
+
     Args:
         fasta: Path to the FASTA file.
         faidx: If True, check for the index file generated by `samtools faidx` (`{fasta}.fai`).
         dictionary: If True, check for the index file generated by `samtools dict` (`{fasta}.dict`).
         bwa: If True, check for the index files generated by `bwa index` (`{fasta}.{suffix}`, for
-            all suffixes in [".amb", ".ann", ".bwt", ".pac", ".sa"]).
+            all suffixes in ["amb", "ann", "bwt", "pac", "sa"]).
 
     Raises:
         AssertionError: If the FASTA or any of the expected index files are missing or not readable.
     """
-    assert_path_is_readable(fasta)
-
-    if faidx:
-        fai_index = Path(f"{fasta}.fai")
-        assert_path_is_readable(fai_index)
+    fai_index = Path(f"{fasta}.fai")
+    assert_path_is_readable(fai_index)
 
     if dictionary:
         dict_index = Path(f"{fasta}.dict")
         assert_path_is_readable(dict_index)
 
     if bwa:
-        suffixes = [".amb", ".ann", ".bwt", ".pac", ".sa"]
+        suffixes = ["amb", "ann", "bwt", "pac", "sa"]
         for suffix in suffixes:
             bwa_index = Path(f"{fasta}.{suffix}")
             assert_path_is_readable(bwa_index)

tests/fgpyo/io/test_io.py

@@ -144,20 +144,22 @@ def test_read_and_write_lines(
         assert int(next(read_back)) == list_to_write[1]
 
 
-@pytest.mark.parametrize("faidx", [True, False])
 @pytest.mark.parametrize("dictionary", [True, False])
 @pytest.mark.parametrize("bwa", [True, False])
-def test_assert_fasta_is_indexed(tmp_path: Path, faidx: bool, dictionary: bool, bwa: bool) -> None:
+def test_assert_fasta_is_indexed(tmp_path: Path, dictionary: bool, bwa: bool) -> None:
     """assert_fasta_is_indexed should verify the presence of the expected index files."""
     fasta = tmp_path / "test.fa"
     fasta.touch()
 
-    if faidx:
-        (tmp_path / "test.fa.fai").touch()
+    (tmp_path / "test.fa.fai").touch()
+
     if dictionary:
         (tmp_path / "test.fa.dict").touch()
     if bwa:
-        for suffix in [".amb", ".ann", ".bwt", ".pac", ".sa"]:
-            (tmp_path / f"test.fa.{suffix}").touch()
+        (tmp_path / "test.fa.amb").touch()
+        (tmp_path / "test.fa.ann").touch()
+        (tmp_path / "test.fa.bwt").touch()
+        (tmp_path / "test.fa.pac").touch()
+        (tmp_path / "test.fa.sa").touch()
 
-    assert_fasta_is_indexed(fasta, faidx=faidx, dictionary=dictionary, bwa=bwa)
+    assert_fasta_is_indexed(fasta, dictionary=dictionary, bwa=bwa)