fixed seq qual length check

[biopieces.git] / bp_bin / join_seq

diff --git a/bp_bin/join_seq b/bp_bin/join_seq
index f071f41d0dcc6a5165267a85f426a719f2a21fa8..5804624df40bbacc26feea12c16919ca0febd594 100755 (executable)
--- a/bp_bin/join_seq
+++ b/bp_bin/join_seq
@@ -33,24 +33,27 @@ require 'maasha/fasta'
 require 'maasha/seq'
 
 casts = []
+casts << {:long=>'delimiter', :short=>'d', :type=>'string', :mandatory=>true, :default=>"", :allowed=>nil, :disallowed=>nil}
 
 options = Biopieces.options_parse(ARGV, casts)
 
-seq = Seq.new(nil, "")
+sequences = []
+seq = Seq.new(seq: "")
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
-    if record.has_key? :SEQ
+    if record[:SEQ]
       unless seq.seq_name 
         seq.seq_name = record[:SEQ_NAME]
       end
-      seq.seq << record[:SEQ]
+      sequences << record[:SEQ]
     end
 
     output.puts record
   end
 
-  if seq.seq != ""
+  unless sequences.empty?
+    seq.seq = sequences.join(options[:delimiter].to_s)
     new_record = seq.to_bp
     new_record[:REC_TYPE] = "JOIN"
     output.puts new_record