rewrite of FASTQ internals

[biopieces.git] / bp_bin / write_fastq_files

diff --git a/bp_bin/write_fastq_files b/bp_bin/write_fastq_files
index a116040b78b5a497b3c0165db8b920bd21d74b28..0b508426eb27761fc218560f93ac0d932bdfcb7f 100755 (executable)
--- a/bp_bin/write_fastq_files
+++ b/bp_bin/write_fastq_files
@@ -32,13 +32,18 @@ require 'maasha/biopieces'
 require 'maasha/fastq'
 require 'pp'
 
+allowed_enc = 'base_33,base_64'
+
 casts = []
-casts << {:long=>'key',       :short=>'k', :type=>'string', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'dir',       :short=>'d', :type=>'dir!',   :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'no_stream', :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'key',       :short=>'k', :type=>'string', :mandatory=>true,  :default=>nil,       :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'dir',       :short=>'d', :type=>'dir!',   :mandatory=>true,  :default=>nil,       :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'no_stream', :short=>'x', :type=>'flag',   :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}
 
 options = Biopieces.options_parse(ARGV, casts)
 
+encoding = options[:encoding].to_sym
+
 key = options[:key].to_sym
 
 fh_hash = {}
@@ -46,7 +51,8 @@ fh_hash = {}
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
     if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES] and record[key]
-      seq = Seq.new_bp(record)
+      entry = Seq.new_bp(record)
+      entry.qual_convert!(:base_33, encoding)
 
       if fh_hash[record[key].to_sym]
         fastq_io = fh_hash[record[key].to_sym]
@@ -56,7 +62,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
         fh_hash[record[key].to_sym] = fastq_io
       end
 
-      fastq_io.puts seq.to_fastq
+      fastq_io.puts entry.to_fastq
     end
 
     output.puts record unless options[:no_stream]