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build.py
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build.py
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import itertools
import os
from cffi import FFI
#TODO: configure this better
samver="1.9"
htslib_dir=os.path.join('submodules', 'samtools-{}'.format(samver), 'htslib-{}'.format(samver))
libraries=['m', 'z', 'lzma', 'bz2', 'pthread', 'curl', 'crypto']
library_dirs=[htslib_dir]
src_dir='src'
ffibuilder = FFI()
ffibuilder.set_source("libmedaka",
r"""
#include "kvec.h"
#include "medaka_bamiter.h"
#include "medaka_common.h"
#include "medaka_counts.h"
#include "medaka_trimbam.h"
#include "medaka_pytrimbam.h"
#include "fastrle.h"
#include "kseq.h"
""",
libraries=libraries,
library_dirs=library_dirs,
include_dirs=[src_dir, htslib_dir],
sources=[os.path.join(src_dir, x) for x in ('medaka_bamiter.c', 'medaka_common.c', 'medaka_counts.c', 'fastrle.c', 'medaka_trimbam.c', 'medaka_pytrimbam.c')],
extra_compile_args=['-std=c99', '-msse3', '-O3'],
extra_objects=['libhts.a']
)
cdef = []
for header in ('medaka_counts.h','fastrle.h', 'medaka_pytrimbam.h'):
with open(os.path.join(src_dir, header), 'r') as fh:
# remove directives
lines = ''.join(x for x in fh.readlines() if not x.startswith('#'))
cdef.append(lines)
ffibuilder.cdef('\n\n'.join(cdef))
if __name__ == "__main__":
ffibuilder.compile(verbose=True)