lib/cheripic/options.rb in cheripic-1.0.0 vs lib/cheripic/options.rb in cheripic-1.1.0

@@ -1,15 +1,15 @@
 #!/usr/bin/env ruby
 
 module Cheripic
 
+  # A class to get default settings and update user settings for parameters
+  # and facilitate retrieval of settings any where in the module
   class Options
 
-    require 'ostruct'
-    # class << self; attr_accessor :params end
-
-    @defaults = {
+    # Default parameter settings
+    @def_settings = {
         :hmes_adjust => 0.5,
         :htlow => 0.2,
         :hthigh => 0.9,
         :mindepth => 6,
         :min_non_ref_count => 3,
@@ -23,19 +23,119 @@
         :filter_out_low_hmes => true,
         :polyploidy => false,
         :bfr_adjust => 0.05,
         :sel_seq_len => 50
     }
-    # @params = OpenStruct.new(@defaults)
 
+    # set defaults as user settings
+    @user_settings = @def_settings
+
+    # A value to adjust calculation of Homozygosity Enrichment Score (HMES)
+    # @return [Float]
+    def self.hmes_adjust
+      @user_settings[:hmes_adjust]
+    end
+
+    # Lower cut off of Allele fraction for categorization of an variant to heterozygous
+    # @return [Float]
+    def self.htlow
+      @user_settings[:htlow]
+    end
+
+    # Higher cut off of Allele fraction for categorization of an variant to heterozygous
+    # @return [Float]
+    def self.hthigh
+      @user_settings[:hthigh]
+    end
+
+    # Minimum read coverage at the variant position to be considered for analysis
+    # @return [Integer]
+    def self.mindepth
+      @user_settings[:mindepth]
+    end
+
+    # Minimum non reference count at the variant position to be considered for analysis
+    # @return [Integer]
+    def self.min_non_ref_count
+      @user_settings[:min_non_ref_count]
+    end
+
+    # Minimum reads supporting an indel at the variant position to be considered for analysis as indel
+    # @return [Integer]
+    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
+    # @return [Boolean]
+    def self.ignore_reference_n
+      @user_settings[:ignore_reference_n]
+    end
+
+    # Minimum alignment mapping quality of the read to be used for bam files
+    # @return [Integer]
+    def self.mapping_quality
+      @user_settings[:mapping_quality]
+    end
+
+    # Minimum aligned base quality at the variant position to be considered for analysis
+    # @return [Integer]
+    def self.base_quality
+      @user_settings[:base_quality]
+    end
+
+    # Threshold for fraction of read bases at variant position below which are ignored as noise
+    # @return [Float]
+    def self.noise
+      @user_settings[:noise]
+    end
+
+    # Option for cross type used for generating bulk population
+    # @note options are either 'back' or 'out'
+    # @return [String]
+    def self.cross_type
+      @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]
+    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]
+    end
+
+    # Option to whether to set the input data is from polyploid or not
+    # @return [Boolean]
+    def self.polyploidy
+      @user_settings[:polyploidy]
+    end
+
+    # A value to adjust calculation of bulk frequency ratio (bfr)
+    # @return [Float]
+    def self.bfr_adjust
+      @user_settings[:bfr_adjust]
+    end
+
+    # Number of nucleotides of sequence to select from each side of the selected variant
+    # @return [Integer]
+    def self.sel_seq_len
+      @user_settings[:sel_seq_len]
+    end
+
+    # Updates the values of options using a hash generated from user inputs
+    # @param newset [Hash] a hash of option names as keys user settings as values
     def self.update(newset)
-      @defaults.merge!(newset)
-      self.params
-      # @params = OpenStruct.new(@defaults)
+      @user_settings = @def_settings.merge(newset)
     end
 
-    def self.params
-      OpenStruct.new(@defaults)
+    # Resets the values of options to defaults
+    def self.defaults
+      @user_settings = @def_settings
     end
 
   end
 
 end