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mappy to support arm64 (#203)

This commit is contained in:
Heng Li 2018-07-24 23:53:02 -04:00
parent ff9917a1c4
commit 99ecdf7b5d
2 changed files with 16 additions and 5 deletions
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1
MANIFEST.in
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@ -4,6 +4,7 @@ include ksw2_dispatch.c
include getopt.c include getopt.c
include main.c include main.c
include README.md include README.md
include sse2neon/emmintrin.h
include python/mappy.c include python/mappy.c
include python/cmappy.h include python/cmappy.h
include python/cmappy.pxd include python/cmappy.pxd

20
setup.py
View File

@ -14,12 +14,22 @@ else: # with Cython
module_src = 'python/mappy.pyx' module_src = 'python/mappy.pyx'
cmdclass['build_ext'] = build_ext cmdclass['build_ext'] = build_ext
import sys import sys, platform
sys.path.append('python') sys.path.append('python')
extra_compile_args = ['-DHAVE_KALLOC']
include_dirs = ["."]
if platform.machine() in ["aarch64", "arm64"]:
include_dirs.append("sse2neon/")
extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
else:
extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
def readme(): def readme():
with open('python/README.rst') as f: with open('python/README.rst') as f:
return f.read() return f.read()
setup( setup(
name = 'mappy', name = 'mappy',
@ -39,8 +49,8 @@ setup(
depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h', depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h', 'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
'python/cmappy.h', 'python/cmappy.pxd'], 'python/cmappy.h', 'python/cmappy.pxd'],
extra_compile_args = ['-DHAVE_KALLOC', '-msse4.1'], # WARNING: ancient x86_64 CPUs don't have SSE4 extra_compile_args = extra_compile_args,
include_dirs = ['.'], include_dirs = include_dirs,
libraries = ['z', 'm', 'pthread'])], libraries = ['z', 'm', 'pthread'])],
classifiers = [ classifiers = [
'Development Status :: 5 - Production/Stable', 'Development Status :: 5 - Production/Stable',