From 195b4b37e1453a170f4b6fbfb15e7e92af512a02 Mon Sep 17 00:00:00 2001
From: Ted Brookings <ted@fulcrumgenomics.com>
Date: Thu, 27 Jul 2023 10:35:31 -0400
Subject: [PATCH] Suppress stderr printing when sam indices are older than sam
 file

---
 fgpyo/io/__init__.py  | 25 +++++++++++++++++++++++++
 fgpyo/sam/__init__.py |  8 ++++++--
 fgpyo/vcf/__init__.py | 25 ++-----------------------
 3 files changed, 33 insertions(+), 25 deletions(-)

diff --git a/fgpyo/io/__init__.py b/fgpyo/io/__init__.py
index a0490899..16b1ed58 100644
--- a/fgpyo/io/__init__.py
+++ b/fgpyo/io/__init__.py
@@ -44,9 +44,12 @@
 import gzip
 import io
 import os
+import sys
+from contextlib import contextmanager
 from pathlib import Path
 from typing import IO
 from typing import Any
+from typing import Generator
 from typing import Iterable
 from typing import Iterator
 from typing import Set
@@ -196,3 +199,25 @@ def write_lines(path: Path, lines_to_write: Iterable[Any]) -> None:
         for line in lines_to_write:
             writer.write(str(line))
             writer.write("\n")
+
+
+@contextmanager
+def redirect_dev_null(
+    file_num: int = sys.stderr.fileno(),
+) -> 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
+    """
+    # open /dev/null for writing
+    f_devnull = os.open(os.devnull, os.O_RDWR)
+    # save old file descriptor and redirect stderr to /dev/null
+    save_stderr = os.dup(file_num)
+    os.dup2(f_devnull, file_num)
+
+    yield
+
+    # restore file descriptor and close devnull
+    os.dup2(save_stderr, file_num)
+    os.close(f_devnull)
diff --git a/fgpyo/sam/__init__.py b/fgpyo/sam/__init__.py
index 508aa96d..0100ce38 100644
--- a/fgpyo/sam/__init__.py
+++ b/fgpyo/sam/__init__.py
@@ -169,6 +169,7 @@
 from pysam import AlignmentFile as SamFile
 from pysam import AlignmentHeader as SamHeader
 
+import fgpyo.io
 from fgpyo.collections import PeekableIterator
 
 SamPath = Union[IO[Any], Path, str]
@@ -259,8 +260,11 @@ def _pysam_open(
     if unmapped and open_for_reading:
         kwargs["check_sq"] = False
 
-    # Open it!
-    return pysam.AlignmentFile(path, **kwargs)
+    # Open it alignment file, suppressing stderr in case index files are older than SAM file
+    with fgpyo.io.redirect_dev_null():
+        alignment_file = pysam.AlignmentFile(path, **kwargs)
+    # now restore stderr and return the alignment file
+    return alignment_file
 
 
 def reader(
diff --git a/fgpyo/vcf/__init__.py b/fgpyo/vcf/__init__.py
index 42621ee3..dfc0ca87 100644
--- a/fgpyo/vcf/__init__.py
+++ b/fgpyo/vcf/__init__.py
@@ -51,8 +51,6 @@
 order via the :func:`~variantbuilder.VariantBuilder.to_sorted_list()` method.
 
 """
-import os
-import sys
 from abc import ABC
 from abc import abstractmethod
 from contextlib import contextmanager
@@ -77,6 +75,7 @@
 from pysam import VariantFile as VcfWriter
 from pysam import VariantHeader
 
+import fgpyo.io
 from fgpyo.sam.builder import SamBuilder
 
 Variant = TypeVar("Variant")
@@ -143,26 +142,6 @@ class VcfFieldNumber(Enum):
     UNKNOWN = "."
 
 
-@contextmanager
-def redirect_dev_null(file_num: int = sys.stderr.fileno()) -> 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
-    """
-    # open /dev/null for writing
-    f_devnull = os.open(os.devnull, os.O_RDWR)
-    # save old file descriptor and redirect stderr to /dev/null
-    save_stderr = os.dup(file_num)
-    os.dup2(f_devnull, file_num)
-
-    yield
-
-    # restore file descriptor and close devnull
-    os.dup2(save_stderr, file_num)
-    os.close(f_devnull)
-
-
 @contextmanager
 def reader(path: VcfPath) -> Generator[VcfReader, None, None]:
     """Opens the given path for VCF reading
@@ -171,7 +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 redirect_dev_null():
+        with fgpyo.io.redirect_dev_null():
             # 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