bin/polymarker.rb in bio-polyploid-tools-0.7.2 vs bin/polymarker.rb in bio-polyploid-tools-0.7.3

@@ -35,10 +35,15 @@
 arm_selection_functions[:arm_selection_morex] = lambda do | contig_name |
   ret = contig_name.split(':')[0].split("_")[1];       
   return ret
 end
 
+arm_selection_functions[:scaffold] = lambda do | contig_name |
+  ret = contig_name;       
+  return ret
+end
+
 def validate_files(o)
 
   [
     o[:path_to_contigs], 
     o[:marker_list], 
@@ -111,10 +116,10 @@
   
   opts.on("-e", "--exonerate_model MODEL", "Model to be used in exonerate to search for the contigs") do |o|
      options[:model] = o
   end
 
-  opts.on("-a", "--arm_selection arm_selection_embl|arm_selection_morex|arm_selection_first_two", "Function to decide the chromome arm") do |o|
+  opts.on("-a", "--arm_selection arm_selection_embl|arm_selection_morex|arm_selection_first_two|scaffold", "Function to decide the chromome arm") do |o|
     options[:arm_selection] = arm_selection_functions[o.to_sym];
    end
   
   opts.on("-p", "--primer_3_preferences FILE", "file with preferences to be sent to primer3") do |o|
     options[:primer_3_preferences] = Bio::DB::Primer3.read_primer_preferences(o, options[:primer_3_preferences] )
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