old_contents: #!/usr/bin/env python
  # Written by Soo Lee and Carl Vitzthum
  # This code is based on the following open-source projects:
  # pytabix (https://github.com/slowkow/pytabix)
  # pysam (https://github.com/pysam-developers)
  # The Github repo for this project is:
  # https://github.com/4dn-dcic/pairix
  # IMPORTANT: use Python 2.7 or above for this package
  
  from setuptools import setup, find_packages, Extension
  
  EXT_MODULES = [
      Extension("pypairix",
          sources=[
              "src/bgzf.c", "src/bgzip.c", "src/index.c",
              "src/knetfile.c", "src/kstring.c",
              "src/pairixmodule.c"
          ],
          include_dirs=["src"],
          libraries=["z"],
          define_macros=[("_FILE_OFFSET_BITS", 64), ("_USE_KNETFILE", 1)]
      )
  ]
  
  setup(
      name = "pypairix",
      version = "0.0.5",
      description = """
          Pypairix is a Python module for fast querying on a pairix-indexed bgzipped text file that contains a pair of genomic coordinates per line.\n
          Input file : bgzipped text file, first sorted by two chromosome columns and then by the first position column. The file should accompany an index file (.px2) created with pairix (https://github.com/4dn-dcic/pairix).\n\n
          Pypairix works with Python >=2.7.\n
          Dependency: python-devel (python-dev for ubuntu), zlib (zlib1g-dev for ubuntu) if not already installed.\n\n
          Please reference the README for more information (https://github.com/4dn-dcic/pairix/blob/master/README.md)
          """,
      url = "https://github.com/4dn-dcic/pairix",
      download_url = "https://github.com/4dn-dcic/pairix/tarball/0.0.5",
      author = "Soo Lee, Carl Vitzthum",
      author_email = "duplexa@gmail.com",
      license = "MIT",
      keywords = ["pairix","tabix", "bgzip", "bioinformatics", "genomics","hi-c"],
      packages = find_packages(),
      package_data = { "": ["*.gz", "*.gz.px2"] },
      ext_modules = EXT_MODULES,
      test_suite = "test",
      classifiers = [
          "Programming Language :: Python :: 2.7",
          "Programming Language :: Python :: 3",
          "Development Status :: 4 - Beta",
          "Intended Audience :: Developers",
          "Intended Audience :: Science/Research",
          "License :: OSI Approved :: MIT License",
          "Operating System :: OS Independent",
          "Programming Language :: C",
          "Topic :: Software Development :: Libraries :: Python Modules",
          "Topic :: Scientific/Engineering :: Bio-Informatics"
      ]
  )
  
new_contents: #!/usr/bin/env python
  # Written by Soo Lee and Carl Vitzthum
  # This code is based on the following open-source projects:
  # pytabix (https://github.com/slowkow/pytabix)
  # pysam (https://github.com/pysam-developers)
  # The Github repo for this project is:
  # https://github.com/4dn-dcic/pairix
  # IMPORTANT: use Python 2.7 or above for this package
  
  from setuptools import setup, find_packages, Extension
  
  EXT_MODULES = [
      Extension("pypairix",
          sources=[
              "src/bgzf.c", "src/bgzip.c", "src/index.c",
              "src/knetfile.c", "src/kstring.c",
              "src/pairixmodule.c"
          ],
          include_dirs=["src"],
          libraries=["z"],
          define_macros=[("_FILE_OFFSET_BITS", 64), ("_USE_KNETFILE", 1)]
      )
  ]
  
  setup(
      name = "pypairix",
      version = "0.0.6",
      description = """
          Pypairix is a Python module for fast querying on a pairix-indexed bgzipped text file that contains a pair of genomic coordinates per line.\n
          Input file : bgzipped text file, first sorted by two chromosome columns and then by the first position column. The file should accompany an index file (.px2) created with pairix (https://github.com/4dn-dcic/pairix).\n\n
          Pypairix works with Python >=2.7.\n
          Dependency: python-devel (python-dev for ubuntu), zlib (zlib1g-dev for ubuntu) if not already installed.\n\n
          Please reference the README for more information (https://github.com/4dn-dcic/pairix/blob/master/README.md)
          """,
      url = "https://github.com/4dn-dcic/pairix",
      download_url = "https://github.com/4dn-dcic/pairix/tarball/0.0.6",
      author = "Soo Lee, Carl Vitzthum",
      author_email = "duplexa@gmail.com",
      license = "MIT",
      keywords = ["pairix","tabix", "bgzip", "bioinformatics", "genomics","hi-c"],
      packages = find_packages(),
      package_data = { "": ["*.gz", "*.gz.px2"] },
      ext_modules = EXT_MODULES,
      test_suite = "test",
      classifiers = [
          "Programming Language :: Python :: 2.7",
          "Programming Language :: Python :: 3",
          "Development Status :: 4 - Beta",
          "Intended Audience :: Developers",
          "Intended Audience :: Science/Research",
          "License :: OSI Approved :: MIT License",
          "Operating System :: OS Independent",
          "Programming Language :: C",
          "Topic :: Software Development :: Libraries :: Python Modules",
          "Topic :: Scientific/Engineering :: Bio-Informatics"
      ]
  )
  
subject: Update to 0.0.6 in setup.py