cmd.rb in cheripic-1.2.7

- old
+ new

@@ -68,14 +68,14 @@
         opt :hmes_adjust, 'factor added to snp count of each contig to adjust for hme score calculations',
             :type => Float,
             :default => 0.5
         opt :htlow, 'lower level for categorizing heterozygosity',
             :type => Float,
-            :default => 0.2
+            :default => 0.25
         opt :hthigh, 'high level for categorizing heterozygosity',
             :type => Float,
-            :default => 0.9
+            :default => 0.75
         opt :mindepth, 'minimum read depth at a position to consider for variant calls',
             :type => Integer,
             :default => 6
         opt :max_d_multiple, "multiplication factor for average coverage to calculate maximum read coverage
 if set zero no calculation will be made from bam file.\nsetting this value will override user set max depth",
@@ -233,31 +233,45 @@
       check_input_files(inputfiles)
     end
 
     # checks if input files are valid
     def check_input_files(inputfiles)
-      check = 0
       inputfiles.each_key do | type |
         inputfiles[type].flatten!
+        check = 0
         inputfiles[type].each do | symbol |
-          if @options[symbol]
+          if @options[symbol] == nil or @options[symbol] == ''
+            if type == :required
+              raise CheripicArgError.new "Options #{inputfiles}, all must be specified. Try --help for further help."
+            end
+          else
             file = @options[symbol]
-            @options[symbol] = File.expand_path(file)
-            next if type == :optional
-            if type == :required and not File.exist?(file)
-              raise CheripicIOError.new "#{symbol} file, #{file} does not exist: "
-            elsif type == :either and File.exist?(file)
-              check = 1
+            if symbol == :bg_bulk or symbol == :bg_bulk_vcf
+              if file.include? ','
+                @options[symbol] = []
+                file.split(',').each do | infile |
+                  @options[symbol] << File.expand_path(infile)
+                  file_exist?(symbol, infile)
+                end
+              end
+            else
+              @options[symbol] = File.expand_path(file)
+              file_exist?(symbol, file)
             end
-          elsif type == :required
-            raise CheripicArgError.new "Options #{inputfiles}, all must be specified. " +
-                                              'Try --help for further help.'
+            check = 1
           end
         end
         if type == :either and check == 0
           raise CheripicArgError.new "One of the options #{inputfiles}, must be specified. " +
                                        'Try --help for further help.'
         end
+      end
+    end
+
+    def file_exist?(symbol, file)
+      # checks if a given file exists
+      unless File.exist?(file)
+        raise CheripicIOError.new "#{symbol} file, #{file} does not exist!"
       end
     end
 
     # checks if files with output tag name already exists
     def check_output