1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
|
import os
import sys
import sysconfig
from pysam.libchtslib import *
from pysam.libcsamtools import *
from pysam.libcbcftools import *
from pysam.libcutils import *
import pysam.libcutils as libcutils
import pysam.libcfaidx as libcfaidx
from pysam.libcfaidx import *
import pysam.libctabix as libctabix
from pysam.libctabix import *
# import pysam.libctabixproxies as libctabixproxies
# from pysam.libctabixproxies import *
import pysam.libcsamfile as libcsamfile
from pysam.libcsamfile import *
import pysam.libcalignmentfile as libcalignmentfile
from pysam.libcalignmentfile import *
import pysam.libcalignedsegment as libcalignedsegment
from pysam.libcalignedsegment import *
import pysam.libcvcf as libcvcf
from pysam.libcvcf import *
import pysam.libcbcf as libcbcf
from pysam.libcbcf import *
import pysam.libcbgzf as libcbgzf
from pysam.libcbgzf import *
from pysam.utils import SamtoolsError
import pysam.Pileup as Pileup
from pysam.samtools import *
import pysam.config
# export all the symbols from separate modules
__all__ = \
libchtslib.__all__ +\
libcutils.__all__ +\
libctabix.__all__ +\
libcvcf.__all__ +\
libcbcf.__all__ +\
libcbgzf.__all__ +\
libcfaidx.__all__ +\
libctabixproxies.__all__ +\
libcalignmentfile.__all__ +\
libcalignedsegment.__all__ +\
libcsamfile.__all__ +\
["SamtoolsError"] +\
["Pileup"]
from pysam.version import __version__, __samtools_version__
def get_include():
'''return a list of include directories.'''
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
#
# Header files may be stored in different relative locations
# depending on installation mode (e.g., `python setup.py install`,
# `python setup.py develop`. The first entry in each list is
# where develop-mode headers can be found.
#
htslib_possibilities = [os.path.join(dirname, '..', 'htslib'),
os.path.join(dirname, 'include', 'htslib')]
samtool_possibilities = [os.path.join(dirname, '..', 'samtools'),
os.path.join(dirname, 'include', 'samtools')]
includes = [dirname]
for header_locations in [htslib_possibilities, samtool_possibilities]:
for header_location in header_locations:
if os.path.exists(header_location):
includes.append(os.path.abspath(header_location))
break
return includes
def get_defines():
'''return a list of defined compilation parameters.'''
# ('_FILE_OFFSET_BITS', '64'),
# ('_USE_KNETFILE', '')]
return []
def get_libraries():
'''return a list of libraries to link against.'''
# Note that this list does not include libcsamtools.so as there are
# numerous name conflicts with libchtslib.so.
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
pysam_libs = ['libctabixproxies',
'libcfaidx',
'libcsamfile',
'libcvcf',
'libcbcf',
'libctabix']
if pysam.config.HTSLIB == "builtin":
pysam_libs.append('libchtslib')
so = sysconfig.get_config_var('SO')
return [os.path.join(dirname, x + so) for x in pysam_libs]
|
