variants.rb in cheripic-1.2.0

- old
+ new

@@ -117,19 +117,21 @@
       end
       @bfr_frags
     end
 
     # Applies selection procedure on assembly contigs based on the ratio_type provided.
-    # If only_frag_with_vars is set to true then contigs without any variant are discarded for :hme_score
+    # If use_all_contigs is set to false then contigs without any variant are discarded for :hme_score
     # while contigs without any hemisnps are discarded for :bfr_score
-    # If filter_out_low_hmes is set to true then contigs are further filtered based on a cut off value of the score
+    # If include_low_hmes is set to false then contigs are further filtered based on a cut off value of the score
     # @param ratio_type [Symbol] ratio_type is either :hme_score or :bfr_score
     def select_contigs(ratio_type)
       selected_contigs ={}
-      only_frag_with_vars = Options.only_frag_with_vars
+      use_all_contigs = Options.use_all_contigs
       @assembly.each_key do | frag |
-        if only_frag_with_vars
+        if use_all_contigs
+          selected_contigs[frag] = @assembly[frag]
+        else
           if ratio_type == :hme_score
             # selecting fragments which have a variant
             if @assembly[frag].hm_num + @assembly[frag].ht_num > 2 * Options.hmes_adjust
               selected_contigs[frag] = @assembly[frag]
             end
@@ -137,19 +139,17 @@
             # in polyploidy scenario selecting fragments with at least one bfr position
             if @assembly[frag].hemi_num > 0
               selected_contigs[frag] = @assembly[frag]
             end
           end
-        else
-          selected_contigs[frag] = @assembly[frag]
         end
       end
       selected_contigs = filter_contigs(selected_contigs, ratio_type)
-      if only_frag_with_vars
-        logger.info "Selected #{selected_contigs.length} out of #{@assembly.length} fragments with #{ratio_type} score\n"
-      else
+      if use_all_contigs
         logger.info "No filtering was applied to fragments\n"
+      else
+        logger.info "Selected #{selected_contigs.length} out of #{@assembly.length} fragments with #{ratio_type} score\n"
       end
       selected_contigs
     end
 
     # Filters out contigs below a cutoff for selected ratio_type
@@ -169,26 +169,26 @@
     # Cut off value calculation used to filter out low scored contigs.
     #
     # @param ratio_type [Symbol] ratio_type is either :hme_score or :bfr_score
     # @param selected_contigs [Hash] a hash of contigs with selected ratio_type, a subset of assembly hash
     def get_cutoff(selected_contigs, ratio_type)
-      filter_out_low_hmes = Options.filter_out_low_hmes
+      include_low_hmes = Options.include_low_hmes
       # set minimum cut off hme_score or bfr_score to pick fragments with variants
       # calculate min hme score for back or out crossed data or bfr_score for polypoidy data
       # if no filtering applied set cutoff to 1.1
-      if filter_out_low_hmes
+      if include_low_hmes
+        cutoff = 0.0
+      else
         if ratio_type == :hme_score
           adjust = Options.hmes_adjust
           if Options.cross_type == 'back'
             cutoff = (1.0/adjust) + 1.0
           else # outcross
             cutoff = (2.0/adjust) + 1.0
           end
         else # ratio_type is bfr_score
           cutoff = bfr_cutoff(selected_contigs)
         end
-      else
-        cutoff = 0.0
       end
       cutoff
     end
 
     # Cut off value calculation for bfr contigs.