rewrite of FASTQ internals

[biopieces.git] / bp_bin / write_fastq

diff --git a/bp_bin/write_fastq b/bp_bin/write_fastq
index 796e187708e52affcf8747e95149a97e986d62f7..30bdd89cdaca441f1ab15d9d21a329e53abdd16f 100755 (executable)
--- a/bp_bin/write_fastq
+++ b/bp_bin/write_fastq
@@ -31,17 +31,17 @@
 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]
@@ -57,7 +57,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   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