lib/cheripic/options.rb in cheripic-1.2.0 vs lib/cheripic/options.rb in cheripic-1.2.5

@@ -10,10 +10,12 @@
     @def_settings = {
         :hmes_adjust => 0.5,
         :htlow => 0.2,
         :hthigh => 0.9,
         :mindepth => 6,
+        :maxdepth => 0,
+        :max_d_multiple => 5,
         :min_non_ref_count => 3,
         :min_indel_count_support => 3,
         :ambiguous_ref_bases => false,
         :mapping_quality => 20,
         :base_quality => 15,
@@ -49,9 +51,29 @@
 
     # Minimum read coverage at the variant position to be considered for analysis
     # @return [Integer]
     def self.mindepth
       @user_settings[:mindepth]
+    end
+
+    # Maximum read coverage at the variant position to be considered for analysis
+    # @return [Integer]
+    def self.maxdepth
+      @user_settings[:maxdepth]
+    end
+
+    # Setting maximum read coverage at the variant position to be considered for analysis
+    # @param value [Integer] provided integer value will be updated as maxdepth
+    # @return [Integer] updated maxdepth value
+    def self.maxdepth=(value)
+      @user_settings[:maxdepth] = value
+    end
+
+    # Multiplication factor to average coverage to calculate maximum read coverage
+    # at the variant position to be considered for analysis
+    # @return [Integer]
+    def self.max_d_multiple
+      @user_settings[:max_d_multiple]
     end
 
     # Minimum non reference count at the variant position to be considered for analysis
     # @return [Integer]
     def self.min_non_ref_count