allowed_enc = 'base_33,base_64'
casts = []
-casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'data_out', :short=>'o', :type=>'file', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'encoding', :short=>'e', :type=>'string', :mandatory=>false, :default=>'base_33', :allowed=>allowed_enc, :disallowed=>nil}
-casts << {:long=>'compress', :short=>'Z', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {long: 'no_stream', short: 'x', type: 'flag', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'data_out', short: 'o', type: 'file', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'encoding', short: 'e', type: 'string', mandatory: false, default: 'base_33', allowed: allowed_enc, disallowed: nil}
+casts << {long: 'compress', short: 'Z', type: 'string', mandatory: false, default: nil, allowed: "gzip,bzip,bzip2", disallowed: nil}
options = Biopieces.options_parse(ARGV, casts)
encoding = options[:encoding].to_sym
+compress = options[:compress] ? options[:compress].to_sym : nil
+
+raise "--data_out is mandatory for compressed output" if compress and not options[:data_out]
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
- if options[:data_out]
- if options[:compress]
- io_out = Zlib::GzipWriter.open(options[:data_out])
- else
- io_out = Fastq.open(options[:data_out], 'w')
- end
- else
- io_out = $stdout
- end
+ fastq_out = options[:data_out] ? Fastq.open(options[:data_out], 'w', compress: compress) : STDOUT
input.each do |record|
if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
entry = Seq.new_bp(record)
entry.qual_convert!(:base_33, encoding)
- io_out.puts entry.to_fastq
+ fastq_out.puts entry.to_fastq
end
output.puts record unless options[:no_stream]
end
- io_out.close
+ fastq_out.close
end