old_contents: # Copyright (c) 2014. Mount Sinai School of Medicine
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #     http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  
  from __future__ import print_function
  import os
  
  from setuptools import setup
  
  current_directory = os.path.dirname(__file__)
  
  if __name__ == '__main__':
      setup(
          name='varlens',
          packages=["varlens", "varlens.commands", "varlens.read_evidence"],
          version="0.0.1",
          description=(
              "tools for working with at genomic variants and NGS reads"),
          long_description=open('README.rst').read(),
          url="https://github.com/hammerlab/varlens",
          author="Tim O'Donnell",
          license="http://www.apache.org/licenses/LICENSE-2.0.html",
          entry_points={
              'console_scripts': [
                  'varlens-allele-support = varlens.commands.allele_support:run',
                  'varlens-variants = varlens.commands.variants:run',
                  'varlens-reads = varlens.commands.reads:run',
              ],
          },
          classifiers=[
              'Development Status :: 3 - Alpha',
              'Environment :: Console',
              'Operating System :: OS Independent',
              'Intended Audience :: Science/Research',
              'License :: OSI Approved :: Apache Software License',
              'Programming Language :: Python',
              'Topic :: Scientific/Engineering :: Bio-Informatics',
          ],
          install_requires=[
              'numpy',
              'intervaltree',
              'pysam>=0.8.4',
              'typechecks',
              'varcode',
              'pyfaidx',
              'mhctools',
              'topiary',
          ],
      )
  
new_contents: # Copyright (c) 2014. Mount Sinai School of Medicine
  #
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #     http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  
  from __future__ import print_function
  import os
  
  from setuptools import setup
  
  current_directory = os.path.dirname(__file__)
  
  if __name__ == '__main__':
      setup(
          name='varlens',
          packages=["varlens", "varlens.commands", "varlens.read_evidence"],
          version="0.0.1",
          description=(
              "commandline manipulation of genomic variants and NGS reads"),
          long_description=open('README.rst').read(),
          url="https://github.com/hammerlab/varlens",
          author="Tim O'Donnell",
          license="http://www.apache.org/licenses/LICENSE-2.0.html",
          entry_points={
              'console_scripts': [
                  'varlens-allele-support = varlens.commands.allele_support:run',
                  'varlens-variants = varlens.commands.variants:run',
                  'varlens-reads = varlens.commands.reads:run',
              ],
          },
          classifiers=[
              'Development Status :: 3 - Alpha',
              'Environment :: Console',
              'Operating System :: OS Independent',
              'Intended Audience :: Science/Research',
              'License :: OSI Approved :: Apache Software License',
              'Programming Language :: Python',
              'Topic :: Scientific/Engineering :: Bio-Informatics',
          ],
          install_requires=[
              'numpy',
              'intervaltree',
              'pysam>=0.8.4',
              'typechecks',
              'varcode',
              'pyfaidx',
              'mhctools',
              'topiary',
          ],
      )
  
subject: fix typo in setup.py