old_contents: from pysam.libchtslib import *
  
  from pysam.cutils import *
  import pysam.cutils as cutils
  
  import pysam.cfaidx as cfaidx
  from pysam.cfaidx import *
  import pysam.ctabix as ctabix
  from pysam.ctabix import *
  import pysam.csamfile as csamfile
  from pysam.csamfile import *
  import pysam.calignmentfile as calignmentfile
  from pysam.calignmentfile import *
  import pysam.calignedsegment as calignedsegment
  from pysam.calignedsegment import *
  import pysam.cvcf as cvcf
  from pysam.cvcf import *
  import pysam.cbcf as cbcf
  from pysam.cbcf import *
  from pysam.utils import SamtoolsError
  
  import pysam.Pileup as Pileup
  import os
  from pysam.samtools import *
  
  # export all the symbols from separate modules
  __all__ = \
      libchtslib.__all__ +\
      cutils.__all__ +\
      ctabix.__all__ +\
      cvcf.__all__ +\
      cbcf.__all__ +\
      cfaidx.__all__ +\
      calignmentfile.__all__ +\
      calignedsegment.__all__ +\
      csamfile.__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__)))
      return [dirname,
              os.path.join(dirname, 'include', 'htslib'),
              os.path.join(dirname, 'include', 'samtools')]
  
  
  def get_defines():
      '''return a list of defined compilation parameters.'''
      return [('_FILE_OFFSET_BITS', '64'),
              ('_USE_KNETFILE', '')]
  
  
  def get_libraries():
      '''return a list of libraries to link against.'''
      # Note that this list does not include csamtools.so as there are
      # numerous name conflicts with libchtslib.so.
      dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
      return [os.path.join(dirname, x) for x in (
          'libchtslib.so',
          'ctabixproxies.so',
          'cfaidx.so',
          'csamfile.so',
          'cvcf.so',
          'cbcf.so',
          'ctabix.so')]
  
new_contents: from pysam.libchtslib import *
  
  from pysam.cutils import *
  import pysam.cutils as cutils
  
  import pysam.cfaidx as cfaidx
  from pysam.cfaidx import *
  import pysam.ctabix as ctabix
  from pysam.ctabix import *
  import pysam.csamfile as csamfile
  from pysam.csamfile import *
  import pysam.calignmentfile as calignmentfile
  from pysam.calignmentfile import *
  import pysam.calignedsegment as calignedsegment
  from pysam.calignedsegment import *
  import pysam.cvcf as cvcf
  from pysam.cvcf import *
  import pysam.cbcf as cbcf
  from pysam.cbcf import *
  from pysam.utils import SamtoolsError
  
  import pysam.Pileup as Pileup
  import os
  from pysam.samtools import *
  
  # export all the symbols from separate modules
  __all__ = \
      libchtslib.__all__ +\
      cutils.__all__ +\
      ctabix.__all__ +\
      cvcf.__all__ +\
      cbcf.__all__ +\
      cfaidx.__all__ +\
      calignmentfile.__all__ +\
      calignedsegment.__all__ +\
      csamfile.__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.'''
      return [('_FILE_OFFSET_BITS', '64'),
              ('_USE_KNETFILE', '')]
  
  
  def get_libraries():
      '''return a list of libraries to link against.'''
      # Note that this list does not include csamtools.so as there are
      # numerous name conflicts with libchtslib.so.
      dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
      return [os.path.join(dirname, x) for x in (
          'libchtslib.so',
          'ctabixproxies.so',
          'cfaidx.so',
          'csamfile.so',
          'cvcf.so',
          'cbcf.so',
          'ctabix.so')]
  
subject: Return correct paths from get_include() when installed in develop mode.