refactoring of assemble_pairs

[biopieces.git] / bp_bin / shred_seq

diff --git a/bp_bin/shred_seq b/bp_bin/shred_seq
index ffd79cb9252bef5dbf2f95258779c1960ef41cf7..322916426e606dd11259eb6f34757486296e039d 100755 (executable)
--- a/bp_bin/shred_seq
+++ b/bp_bin/shred_seq
@@ -84,8 +84,8 @@ options = Biopieces.options_parse(ARGV, casts)
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
     if record[:SEQ] and record[:SEQ].length >= options[:size]
-      entry      = Seq.new(record[:SEQ_NAME], record[:SEQ], record[:SCORES])
-      entry.type = 'dna'
+      entry      = Seq.new_bp(record)
+      entry.type = :dna
 
       entry.shred(options[:size], options[:coverage]) do |subentry|
         output.puts subentry.to_bp