From 4019e8411b03a2882db2626d6a07e095b55bced6 Mon Sep 17 00:00:00 2001
From: Nils Homer <nh13@users.noreply.github.com>
Date: Fri, 17 Jan 2025 09:54:56 -0800
Subject: [PATCH] chore: add rt to the list of bwa linked libraries (#24)

Also ignore many warnings when compiling bwa
---
 build.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/build.py b/build.py
index e825fcb..1525482 100644
--- a/build.py
+++ b/build.py
@@ -1,4 +1,5 @@
 import multiprocessing
+import platform
 from pathlib import Path
 from typing import List
 
@@ -12,6 +13,8 @@
 link_args = []
 include_dirs = ["bwa", "pybwa"]
 libraries = ['m', 'z', 'pthread']
+if platform == 'Linux':
+    libraries.append("rt")
 library_dirs=['pybwa', 'bwa']
 extra_objects = []
 h_files = []
@@ -20,6 +23,16 @@
     h_files.extend(str(x) for x in Path(root_dir).rglob("*.h"))
     c_files.extend(str(x) for x in Path(root_dir).rglob("*.c") if x.name not in ['example.c', 'main.c'])
 
+if platform.system() != 'Windows':
+    compile_args = [
+        "-Wno-unreachable-code",
+        "-Wno-single-bit-bitfield-constant-conversion",
+        "-Wno-deprecated-declarations",
+        "-Wno-unused",
+        "-Wno-strict-prototypes",
+        "-Wno-sign-compare",
+        "-Wno-error=declaration-after-statement"]
+
 libbwaindex_module = Extension(
     name='pybwa.libbwaindex',
     sources=['pybwa/libbwaindex.pyx'] + c_files,