-casts = []
-casts << {:long=>'adaptor', :short=>'a', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'partial', :short=>'p', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'len', :short=>'l', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>'0'}
-casts << {:long=>'mismatches', :short=>'m', :type=>'uint', :mandatory=>false, :default=>10, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'insertions', :short=>'i', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'deletions', :short=>'d', :type=>'uint', :mandatory=>false, :default=>5, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'cpus', :short=>'c', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>'0'}
-
-BASE_PER_FILE = 10_000_000
-
-options = Biopieces.options_parse(ARGV, casts)
-
-tmpdir = Biopieces.mktmpdir
-file_records = File.join(tmpdir, "data.stream")
-file_pattern = File.join(tmpdir, "pattern.txt")
-
-number_file = 0
-number_seq = 0
-bases = 0
-
-Biopieces.open(options[:stream_in], file_records) do |input, output|
- file_fasta = File.join(tmpdir, "#{number_file}.fna")
- out_fa = Fasta.open(file_fasta, 'w')
-