require 'maasha/biopieces'
require 'maasha/fastq'
-allowed_enc = 'sanger,solexa,illumina1.3,illumina1.5,illumina1.8'
+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=>'illumina1.3', :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=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
options = Biopieces.options_parse(ARGV, casts)
-encoding = options[:encoding].downcase.delete('.')
+encoding = options[:encoding].to_sym
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
if options[:data_out]
input.each do |record|
if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
entry = Seq.new_bp(record)
- entry.convert_scores!('illumina13', encoding)
+ entry.qual_convert!(:base_33, encoding)
io_out.puts entry.to_fastq
end