old_contents: #!/usr/bin/env python
  #
  # -----------------------------------------------------------------------------
  # Copyright (c) 2017 The Regents of the University of California
  #
  # This file is part of kevlar (http://github.com/dib-lab/kevlar) and is
  # licensed under the MIT license: see LICENSE.
  # -----------------------------------------------------------------------------
  
  import pytest
  import sys
  import kevlar
  from kevlar.tests import data_file
  
  
  def test_pico_4(capsys):
      reads = data_file('pico-4.augfastq.gz')
      refr = data_file('human-random-pico.fa.gz')
      arglist = ['alac', '--ksize', '25', reads, refr]
      args = kevlar.cli.parser().parse_args(arglist)
      kevlar.alac.main(args)
      out, err = capsys.readouterr()
  
      msg = 'assembled 22/28 reads from 1 connected component(s) into 1 contig'
      assert msg in err
  
      vcf = ('seq1\t1175768\t.\tT\tC\t.\tPASS\tVW=CCCTGCCATTATAGATGCTAGATTCACATC'
             'TTCATTTATTTTTACTTTT')
      assert vcf.strip() == out.strip()
  
new_contents: #!/usr/bin/env python
  #
  # -----------------------------------------------------------------------------
  # Copyright (c) 2017 The Regents of the University of California
  #
  # This file is part of kevlar (http://github.com/dib-lab/kevlar) and is
  # licensed under the MIT license: see LICENSE.
  # -----------------------------------------------------------------------------
  
  import pytest
  import sys
  import kevlar
  from kevlar.tests import data_file
  
  
  def test_pico_4(capsys):
      reads = data_file('pico-4.augfastq.gz')
      refr = data_file('human-random-pico.fa.gz')
      arglist = ['alac', '--ksize', '25', reads, refr]
      args = kevlar.cli.parser().parse_args(arglist)
      kevlar.alac.main(args)
      out, err = capsys.readouterr()
  
      msg = 'assembled 22/28 reads from 1 connected component(s) into 1 contig'
      assert msg in err
  
      vcf = ('seq1\t1175768\t.\tT\tC\t.\tPASS\tRW=CCCTGCCATTATAGATGCTAGATTTACATC'
             'TTCATTTATTTTTACTTTT;VW=CCCTGCCATTATAGATGCTAGATTCACATCTTCATTTATTTTT'
             'ACTTTT')
      assert vcf.strip() == out.strip()
  
subject: Update test output