corrects infinte annotation columns problem

src/reporting.rb

@@ -236,19 +236,25 @@ def merge_csv(file, index)
     added = false
     my_headers = []
     CSV.foreach(file, headers: true, col_sep: "\t") do |row|
+      # skip if empty line
+      next if row[0].nil? || row[1].nil? || row[0].empty? || row[1].empty?
+      # determine headers
       unless added
         my_headers = (row.headers[2..(row.headers.size)]).collect do |str|
           str + "_annot_#{index}"
         end
         @results_headers.concat my_headers
+        added = true
       end
-      added = true
+      # add additional information to each entry
+      #  note: this can take some time depending on the annotation files size
       @db.add_info({ one: row.headers[0], two: row.headers[1] },
                    { one: row[0], two: row[1] },
                    my_headers,
                    row.values_at[2..(row.headers.size)],
                    my_headers.collect { file })
     end
+    byebug
   end
   #
   #

src/results_db.rb

@@ -102,10 +102,17 @@ def values
     end
   end
 
+  # Add additional information to each row
   def add_info(keys, values, new_col_key, new_col_val, file_origin = nil)
-    header.concat new_col_key
-    file_origin = [new_col_key] if file_origin.nil?
-    header_meaning.concat file_origin
+    file_origin = new_col_key.size.collect { '' } if file_origin.nil?
+    # only add header if it is not yet declared
+    new_col_key.each_with_index do |val, ix|
+      unless header.include?(val)
+        header.concat([val])
+        header_meaning.concat([file_origin[ix]])
+      end
+    end
+    #
     db.values.each do |el|
       new_col_key.each_with_index do |col_key, ix|
         if el[keys[:one]] == values[:one] && el[keys[:two]] == values[:two]