Respond to review comments

fgpyo/io/__init__.py

@@ -202,13 +202,11 @@ def write_lines(path: Path, lines_to_write: Iterable[Any]) -> None:
 
 
 @contextmanager
-def redirect_dev_null(
-    file_num: int = sys.stderr.fileno(),
-) -> Generator[None, None, None]:
+def redirect_to_dev_null(file_num: int) -> Generator[None, None, None]:
     """A context manager that redirects output of file handle to /dev/null
 
     Args:
-        file_num: number of filehandle to redirect. Uses stderr by default
+        file_num: number of filehandle to redirect.
     """
     # open /dev/null for writing
     f_devnull = os.open(os.devnull, os.O_RDWR)
@@ -221,3 +219,10 @@ def redirect_dev_null(
     # restore file descriptor and close devnull
     os.dup2(save_stderr, file_num)
     os.close(f_devnull)
+
+
+@contextmanager
+def suppress_stderr() -> Generator[None, None, None]:
+    """A context manager that redirects output of stderr to /dev/null"""
+    with redirect_to_dev_null(file_num=sys.stderr.fileno()):
+        yield

fgpyo/sam/__init__.py

@@ -261,7 +261,7 @@ def _pysam_open(
         kwargs["check_sq"] = False
 
     # Open it alignment file, suppressing stderr in case index files are older than SAM file
-    with fgpyo.io.redirect_dev_null():
+    with fgpyo.io.suppress_stderr():
         alignment_file = pysam.AlignmentFile(path, **kwargs)
     # now restore stderr and return the alignment file
     return alignment_file

fgpyo/vcf/__init__.py

@@ -150,7 +150,7 @@ def reader(path: VcfPath) -> Generator[VcfReader, None, None]:
         path: the path to a VCF, or an open file handle
     """
     if isinstance(path, (str, Path, TextIO)):
-        with fgpyo.io.redirect_dev_null():
+        with fgpyo.io.suppress_stderr():
             # to avoid spamming log about index older than vcf, redirect stderr to /dev/null: only
             # when first opening the file
             _reader = VariantFile(path, mode="r")  # type: ignore