bin/profiles2phenopacket.rb in pets-0.2.4 vs bin/profiles2phenopacket.rb in pets-0.2.5

@@ -25,34 +25,10 @@
 
 options = {}
 OptionParser.new do |opts|
   opts.banner = "Usage: #{__FILE__} [options]"
 
-  options[:chromosome_col] = nil
-  opts.on("-c", "--chromosome_col INTEGER/STRING", "Column name if header is true, otherwise 0-based position of the column with the chromosome") do |data|
-    options[:chromosome_col] = data
-  end
-
-  options[:id_col] = nil
-  opts.on("-d", "--pat_id_col INTEGER/STRING", "Column name if header is true, otherwise 0-based position of the column with the patient id") do |data|
-    options[:id_col] = data
-  end
-
-  options[:end_col] = nil
-  opts.on("-e", "--end_col INTEGER/STRING", "Column name if header is true, otherwise 0-based position of the column with the end mutation coordinate") do |data|
-    options[:end_col] = data
-  end
-
-  options[:genome_assembly] = 'hg38'
-  opts.on("-G", "--genome_assembly STRING", "Genome assembly version. Please choose between hg18, hg19 and hg38. Default hg38") do |data|
-    options[:genome_assembly] = data
-  end
-
-  options[:header] = true
-  #chr\tstart\tstop
-  opts.on("-H", "--header", "Set if the file has a line header. Default true") do 
-    options[:header] = false
-  end
+  eval(File.open(COMMON_OPTPARSE).read)
 
   options[:input_file] = nil
   opts.on("-i", "--input_file PATH", "Input file with patient data") do |data|
     options[:input_file] = data
   end