old_contents: #!/usr/bin/env python
  
  from distutils.core import setup
  
  setup(name='ngsutils',
        version='0.5.2c',
        description='NGSUtils - Various utilities for working with NGS data',
        author='Marcus Breese',
        author_email='mbreese@stanford.edu',
        url='http://ngsutils.org',
        packages=['ngsutils', 'ngsutils.bam', 'ngsutils.bed', 'ngsutils.fastq', 'ngsutils.gtf', 'ngsutils.support', 'ngsutils.ngs'],
  #      scripts=['bin/ngsutils', 'bin/fastqutils', 'bin/bamutils', 'bin/bedutils', 'bin/gtfutils'],
        install_requires = ['pysam>=0.4.1', 'coverage>=3.5.3', 'eta>=0.9', 'swalign>=0.2']
       )
  
new_contents: #!/usr/bin/env python
  
  from distutils.core import setup
  
  setup(name='ngsutils',
        version='0.5.2c',
        description='NGSUtils - Various utilities for working with NGS data',
        author='Marcus Breese',
        author_email='mbreese@stanford.edu',
        url='http://ngsutils.org',
        packages=['ngsutils', 'ngsutils.bam', 'ngsutils.bed', 'ngsutils.fastq', 'ngsutils.gtf', 'ngsutils.support', 'ngsutils.ngs'],
  #      scripts=['bin/ngsutils', 'bin/fastqutils', 'bin/bamutils', 'bin/bedutils', 'bin/gtfutils'],
        install_requires = ['pysam==0.7.5', 'coverage>=3.5.3', 'eta>=0.9', 'swalign>=0.2']
       )
  
subject: settle at pysam 0.7.5 until bug fixed.