lib/cheripic/options.rb in cheripic-1.1.0 vs lib/cheripic/options.rb in cheripic-1.2.0

@@ -12,17 +12,17 @@
         :htlow => 0.2,
         :hthigh => 0.9,
         :mindepth => 6,
         :min_non_ref_count => 3,
         :min_indel_count_support => 3,
-        :ignore_reference_n => true,
+        :ambiguous_ref_bases => false,
         :mapping_quality => 20,
         :base_quality => 15,
         :noise => 0.1,
         :cross_type => 'back',
-        :only_frag_with_vars => true,
-        :filter_out_low_hmes => true,
+        :use_all_contigs => false,
+        :include_low_hmes => false,
         :polyploidy => false,
         :bfr_adjust => 0.05,
         :sel_seq_len => 50
     }
 
@@ -64,13 +64,14 @@
     def self.min_indel_count_support
       @user_settings[:min_indel_count_support]
     end
 
     # Option to whether to ignore or consider the reference positions which are ambiguous
+    # @note switching option name here so Pileup options are same
     # @return [Boolean]
     def self.ignore_reference_n
-      @user_settings[:ignore_reference_n]
+      @user_settings[:ambiguous_ref_bases] ? false : true
     end
 
     # Minimum alignment mapping quality of the read to be used for bam files
     # @return [Integer]
     def self.mapping_quality
@@ -96,17 +97,17 @@
       @user_settings[:cross_type]
     end
 
     # Option to whether to ignore or consider the contigs with out any variants
     # @return [Boolean]
-    def self.only_frag_with_vars
-      @user_settings[:only_frag_with_vars]
+    def self.use_all_contigs
+      @user_settings[:use_all_contigs]
     end
 
     # Option to whether to ignore or consider the contigs with low HME score
     # @return [Boolean]
-    def self.filter_out_low_hmes
-      @user_settings[:filter_out_low_hmes]
+    def self.include_low_hmes
+      @user_settings[:include_low_hmes]
     end
 
     # Option to whether to set the input data is from polyploid or not
     # @return [Boolean]
     def self.polyploidy