# Test mhmms with --maxseqs option (r1635)
&test('mhmms1', 'test --maxseqs option',
  'mhmms', '',
  [
    '--maxseqs', 
    3, 
    '--quiet', 
    make_test_src_path('mhmm/crp0.linear.mhmm'), 
    make_test_src_path('common/crp0.s')
  ],
  [
    {
      output => '-', 
      reference => make_test_src_path('mhmms/r1635.maxseqs.mhmms'), 
      type => 'text'
    }
  ],
  'results/mhmms1'
);

# Test mhmms with --global option (r1635)
&test('mhmms2', 'test --global option',
  'mhmms', '',
  [
    '--global', 
    '--quiet', 
    make_test_src_path('mhmm/lipo.linear.mhmm'), 
    make_test_src_path('common/lipo.fasta')
  ],
  [
    {
      output => '-', 
      reference => 'make_test_src_path(mhmms/r1635.global.mhmms'), 
      type => 'text'
    }
  ],
  'results/mhmms2'
);

# Test mhmms for bug where runs of 
# spacer states are scored as matches (r1635).
# With theses input files mhmms should find no matches.
&test('mhmms3', 'test runs of spacer states scored as matches',
  'mhmms', '', 
  [
    '--quiet', 
    '--motif-scoring', 
    make_test_src_path('mhmm/lipo.linear.mhmm'), 
    make_test_src_path('mhmms/r1635.fasta')
  ],
  [
    {
      output => '-', 
      reference => make_test_src_path('mhmms/r1635.mhmms'), 
      type => 'text'
    }
  ],
  'results/mhmms3'
);

# Test mhmms for segmentation fault when --motif-scoring option 
# is used. (r1584)
&test('mhmms4', 'test --motif-scoring option',
  'mhmms', '',
  [
    '--motif-scoring', 
    '--quiet', 
    'mhmms/r1584.hmm', 
    'mhmms/r1584.fasta'
  ],
  [
    {
      output => '-', 
      reference => 'mhmms/r1584.mhmms', 
      type => 'text'
    }
  ],
  'results/mhmms4'
);

