old_contents: import os, sys, glob
  import pysam
  
  name = 'genda'
  version = '0.1'
  
  from distutils.core import setup
  from distutils.extension import Extension
  
  try:
      from Cython.Distutils import build_ext
  except ImportError:
      use_cython = False
      print("Cython not found")
  else:
      use_cython = True
  
  cmdclass = {}
  ext_modules = []
  
  if use_cython:
      print('using cython')
      ext_modules += [
          Extension("genda.transcripts.exon_utils",
                    ["genda/transcripts/exon_utils.pyx" ],),
          Extension("genda.pysam_callbacks.allele_counter",
              ["genda/pysam_callbacks/allele_counter.pyx"],
              include_dirs=pysam.get_include(),
              define_macros=pysam.get_defines()),
      ]
      print(ext_modules)
      cmdclass.update({'build_ext': build_ext})
  else:
      ext_modules += [
          Extension("genda.transcripts.exon_utils",
                    ["genda/transcripts/exon_utils.c"]),
          Extension("genda.pysam_callbacks.allele_counter",
              ["genda/pysam_callbacks.allele_counter.c"]),
          Extension("genda.pysam_callbacks.gene_counter",
              ["genda/pysam_callbacks.allele_counter.c"]),
      ]
  
  
  metadata = {'name':name,
              'version': version,
              'cmdclass': cmdclass,
              'ext_modules': ext_modules,
              'scripts': glob.glob('scripts/*.py'),
              'description':'genda',
              'author':'Jeffrey Hsu',
              'packages':['genda', 'genda.stats',
                          'genda.parsing','genda.formats',
                          'genda.pysam_callbacks',
                         'genda.transcripts', 'genda.AEI'],
  }
  
  
  if __name__ == '__main__':
      dist = setup(**metadata)
      """
          Extension("genda.pysam_callbacks.gene_counter",
              ["genda/pysam_callbacks/gene_counter.pyx"],
              include_dirs=pysam.get_include()),
      """
  
new_contents: import os, sys, glob
  import numpy
  import pysam
  
  name = 'genda'
  version = '0.1'
  
  from distutils.core import setup
  from distutils.extension import Extension
  
  try:
      from Cython.Distutils import build_ext
  except ImportError:
      use_cython = False
      print("Cython not found")
  else:
      use_cython = True
  
  cmdclass = {}
  ext_modules = []
  includes = pysam.get_include()
  includes.append(numpy.get_include())
  
  
  if use_cython:
      print('**********using cython*********')
      ext_modules += [
          Extension("genda.transcripts.exon_utils",
                    ["genda/transcripts/exon_utils.pyx" ], 
                    include_dirs=includes),
  
          Extension("genda.pysam_callbacks.allele_counter",
              ["genda/pysam_callbacks/allele_counter.pyx"],
              include_dirs=includes,
              define_macros=pysam.get_defines()),
      ]
      print(ext_modules)
      cmdclass.update({'build_ext': build_ext})
  else:
      ext_modules += [
          Extension("genda.transcripts.exon_utils",
                    ["genda/transcripts/exon_utils.c"]),
          Extension("genda.pysam_callbacks.allele_counter",
              ["genda/pysam_callbacks.allele_counter.c"]),
          Extension("genda.pysam_callbacks.gene_counter",
              ["genda/pysam_callbacks.allele_counter.c"]),
      ]
  
  
  metadata = {'name':name,
              'version': version,
              'cmdclass': cmdclass,
              'ext_modules': ext_modules,
              'scripts': glob.glob('scripts/*.py'),
              'description':'genda',
              'author':'Jeffrey Hsu',
              'packages':['genda', 'genda.stats',
                          'genda.parsing','genda.formats',
                          'genda.pysam_callbacks',
                         'genda.transcripts', 'genda.AEI'],
  }
  
  
  if __name__ == '__main__':
      dist = setup(**metadata)
      """
          Extension("genda.pysam_callbacks.gene_counter",
              ["genda/pysam_callbacks/gene_counter.pyx"],
              include_dirs=pysam.get_include()),
      """
  
subject: include fixes