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1 #!/usr/bin/env python2.7
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2 # Setup for ezBAMQC, utilities for the Sequence Alignment/Map format.
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3 #
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4 # Copyright (C) 2015 Bioinformatics Shared Resource, CSHL.
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5 # Portions copyright (C) 2015 Cold Spring Harbor Laboratory.
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6 #
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7 # Permission is hereby granted, free of charge, to any person obtaining a copy
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8 # of this software and associated documentation files (the "Software"), to deal
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9 # in the Software without restriction, including without limitation the rights
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10 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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11 # copies of the Software, and to permit persons to whom the Software is
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12 # furnished to do so, subject to the following conditions:
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13 #
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14 # The above copyright notice and this permission notice shall be included in
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15 # all copies or substantial portions of the Software.
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16 #
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17 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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18 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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19 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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20 # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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21 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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22 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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23 # DEALINGS IN THE SOFTWARE.
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24
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25 import argparse
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26 import sys, os, glob, fnmatch
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27
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28 ## Added 10 Jan 2008
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29 from distutils.core import setup, Extension
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30 import distutils.command.install_data
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31
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32 ## Code borrowed from wxPython's setup and config files
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33 ## Thanks to Robin Dunn for the suggestion.
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34 ## I am not 100% sure what's going on, but it works!
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35 def opj(*args):
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36 path = os.path.join(*args)
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37 return os.path.normpath(path)
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38
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39 ## Added 10 Jan 2008
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40 # Specializations of some distutils command classes
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41 class wx_smart_install_data(distutils.command.install_data.install_data):
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42 """need to change self.install_dir to the actual library dir"""
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43 def run(self):
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44 install_cmd = self.get_finalized_command('install')
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45 self.install_dir = getattr(install_cmd, 'install_lib')
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46 return distutils.command.install_data.install_data.run(self)
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47
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48 def find_data_files(srcdir, *wildcards, **kw):
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49 # get a list of all files under the srcdir matching wildcards,
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50 # returned in a format to be used for install_data
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51 def walk_helper(arg, dirname, files):
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52 if '.svn' in dirname:
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53 return
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54 names = []
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55 lst, wildcards = arg
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56 for wc in wildcards:
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57 wc_name = opj(dirname, wc)
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58 for f in files:
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59 filename = opj(dirname, f)
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60
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61 if fnmatch.fnmatch(filename, wc_name) and not os.path.isdir(filename):
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62 names.append(filename)
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63 if names:
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64 lst.append( (dirname, names ) )
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65
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66 file_list = []
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67 recursive = kw.get('recursive', True)
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68 if recursive:
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69 os.path.walk(srcdir, walk_helper, (file_list, wildcards))
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70 else:
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71 walk_helper((file_list, wildcards),
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72 srcdir,
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73 [os.path.basename(f) for f in glob.glob(opj(srcdir, '*'))])
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74 return file_list
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75
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76 ## This is a list of files to install, and where:
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77 ## Make sure the MANIFEST.in file points to all the right
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78 ## directories too.
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79 files = find_data_files('ezBAMQC/', '*.*')
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80
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81 from distutils.core import setup
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82
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83 def readme():
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84 with open('README.rst') as f:
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85 return f.read()
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86
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87 if sys.version_info[0] != 2 or sys.version_info[1] < 7:
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88 print >> sys.stderr, "ERROR: ezBAMQC requires Python 2.7"
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89 sys.exit()
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90
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91 BAMQC_HEADER = [
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92 'src/ezBAMQC/Constants.h',
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93 'src/ezBAMQC/Coverage_prof.h',
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94 'src/ezBAMQC/GeneFeatures.h',
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95 'src/ezBAMQC/InnerDist_prof.h',
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96 'src/ezBAMQC/IntervalTree.h',
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97 'src/ezBAMQC/Mappability.h',
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98 'src/ezBAMQC/parseBAM.h',
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99 'src/ezBAMQC/ReadDup_prof.h',
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100 'src/ezBAMQC/Results.h',
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101 'src/ezBAMQC/rRNA.h'
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102 ]
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103
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104 BAMQC_SOURCE = [
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105 'src/ezBAMQC/Coverage_prof.cpp',
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106 'src/ezBAMQC/GeneFeatures.cpp',
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107 'src/ezBAMQC/InnerDist_prof.cpp',
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108 'src/ezBAMQC/IntervalTree.cpp',
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109 'src/ezBAMQC/Mappability.cpp',
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110 'src/ezBAMQC/parseBAM.cpp',
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111 'src/ezBAMQC/ReadDup_prof.cpp',
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112 'src/ezBAMQC/Results.cpp',
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113 'src/ezBAMQC/rRNA.cpp'
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114 ]
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115
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116 ###TODO HAVE TO SPLIT INTO TWO AND MAKE THE A FILE
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117 HTSLIB_PUBLIC_HEADERS = [
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118 'src/htslib/bgzf.h',
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119 'src/htslib/faidx.h',
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120 'src/htslib/hfile.h',
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121 'src/htslib/hts.h',
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122 'src/htslib/hts_defs.h',
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123 'src/htslib/khash.h',
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124 'src/htslib/klist.h',
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125 'src/htslib/knetfile.h',
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126 'src/htslib/kseq.h',
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127 'src/htslib/ksort.h',
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128 'src/htslib/kstring.h',
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129 'src/htslib/regidx.h',
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130 'src/htslib/sam.h',
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131 'src/htslib/synced_bcf_reader.h',
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132 'src/htslib/tbx.h',
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133 'src/htslib/vcf.h',
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134 'src/htslib/vcf_sweep.h',
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135 'src/htslib/vcfutils.h'
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136 ]
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137
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138
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139 HTSLIB = [
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140 'src/htslib/bgzf.c',
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141 'src/htslib/faidx.c',
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142 'src/htslib/hfile.c',
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143 'src/htslib/hfile_net.c',
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144 'src/htslib/hts.c',
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145 'src/htslib/kfunc.c',
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146 'src/htslib/knetfile.c',
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147 'src/htslib/kstring.c',
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148 'src/htslib/regidx.c',
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149 'src/htslib/sam.c',
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150 'src/htslib/synced_bcf_reader.c',
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151 'src/htslib/tbx.c',
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152 'src/htslib/vcf.c',
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153 'src/htslib/vcfutils.c',
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154 'src/htslib/cram/cram_codecs.c',
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155 'src/htslib/cram/cram_decode.c',
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156 'src/htslib/cram/cram_encode.c',
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157 'src/htslib/cram/cram_index.c',
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158 'src/htslib/cram/cram_io.c',
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159 'src/htslib/cram/cram_samtools.c',
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160 'src/htslib/cram/cram_stats.c',
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161 'src/htslib/cram/files.c',
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162 'src/htslib/cram/mFILE.c',
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163 'src/htslib/cram/md5.c',
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164 'src/htslib/cram/open_trace_file.c',
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165 'src/htslib/cram/pooled_alloc.c',
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166 'src/htslib/cram/rANS_static.c',
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167 'src/htslib/cram/sam_header.c',
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168 'src/htslib/cram/string_alloc.c',
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169 'src/htslib/cram/thread_pool.c',
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170 'src/htslib/cram/vlen.c',
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171 'src/htslib/cram/zfio.c'
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172 ]
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173
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174 BAMqc_CFLAGS = ['-fpermissive','-O3','-std=c++11','-Wno-error=declaration-after-statement']
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175 BAMqc_DFLAGS = [('_FILE_OFFSET_BITS','64'),('_LARGEFILE64_SOURCE',''),('_CURSES_LIB','1')]
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176 BAMqc_INCLUDES = ['./src/htslib']
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177 BAMqc_HEADERS = ['./src/ezBAMQC']
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178 BAMqc_EXTRA = ['build/lib.linux-x86_64-2.7/htslib.so']
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179
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180 htslib_CFLAGS = ['-Wno-error=declaration-after-statement']
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181 htslib_HEADERS = ['./src/htslib','./src/htslib/htslib','./src/htslib/cram']
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182 htslib_DFLAGS = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')]
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183
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184 setup(name = "ezBAMQC",
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185 version = "0.6.7",
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186 description = 'Quality control tools for NGS alignment file',
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187 keywords = 'Quality control BAM file',
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188 # make sure to add all the nessacary requires
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189 dependency_links=['https://gcc.gnu.org/gcc-4.8/','https://www.r-project.org/','https://cran.r-project.org/web/packages/corrplot/'],
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190 cmdclass = { 'install_data': wx_smart_install_data },
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191 scripts = ["ezBAMQC"],
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192 author = "Ying Jin",
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193 author_email ="yjin@cshl.edu",
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194 license='GPLv3',
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195 platforms = ['Linux'],
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196 url='http://hammelllab.labsites.cshl.edu/software#BAMqc',
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197 long_description=readme(),
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198 classifiers=[
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199 'Development Status :: 4 - Beta',
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200 'Natural Language :: English',
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201 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
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202 'Topic :: Scientific/Engineering :: Bio-Informatics',
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203 'Intended Audience :: Science/Research',
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204 'Programming Language :: Python :: 2.7',
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205 'Programming Language :: C++',
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206 'Operating System :: Unix',
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207 ],
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208 zip_safe = False,
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209 include_package_data=True,
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210 ext_modules = [
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211 Extension('htslib',
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212 sources = HTSLIB,
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213 include_dirs = htslib_HEADERS,
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214 extra_compile_args = htslib_CFLAGS,
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215 define_macros = htslib_DFLAGS,
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216 libraries=['z']
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217 ),
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218 Extension('libBAMqc',
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219 sources = BAMQC_SOURCE,
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220 extra_compile_args = BAMqc_CFLAGS,
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221 include_dirs = BAMqc_HEADERS + htslib_HEADERS,
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222 extra_objects = BAMqc_EXTRA,
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223 define_macros = BAMqc_DFLAGS
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224 )
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225 ]
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226 )
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