class Cheripic::Options
A class to get default settings and update user settings for parameters and facilitate retrieval of settings any where in the module
Public Class Methods
Minimum aligned base quality at the variant position to be considered for analysis @return [Integer]
# File lib/cheripic/options.rb, line 105 def self.base_quality @user_settings[:base_quality] end
A value to adjust calculation of bulk frequency ratio (bfr) @return [Float]
# File lib/cheripic/options.rb, line 142 def self.bfr_adjust @user_settings[:bfr_adjust] end
Option for cross type used for generating bulk population @note options are either 'back' or 'out' @return [String]
# File lib/cheripic/options.rb, line 118 def self.cross_type @user_settings[:cross_type] end
Resets the values of options to defaults
# File lib/cheripic/options.rb, line 164 def self.current_values @user_settings end
Resets the values of options to defaults
# File lib/cheripic/options.rb, line 159 def self.defaults @user_settings = @def_settings end
A value to adjust calculation of Homozygosity Enrichment Score (HMES) @return [Float]
# File lib/cheripic/options.rb, line 36 def self.hmes_adjust @user_settings[:hmes_adjust] end
Higher cut off of Allele fraction for categorization of an variant to heterozygous @return [Float]
# File lib/cheripic/options.rb, line 48 def self.hthigh @user_settings[:hthigh] end
Lower cut off of Allele fraction for categorization of an variant to heterozygous @return [Float]
# File lib/cheripic/options.rb, line 42 def self.htlow @user_settings[:htlow] 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]
# File lib/cheripic/options.rb, line 93 def self.ignore_reference_n @user_settings[:ambiguous_ref_bases] ? false : true end
Option to whether to ignore or consider the contigs with low HME score @return [Boolean]
# File lib/cheripic/options.rb, line 130 def self.include_low_hmes @user_settings[:include_low_hmes] end
Minimum alignment mapping quality of the read to be used for bam files @return [Integer]
# File lib/cheripic/options.rb, line 99 def self.mapping_quality @user_settings[:mapping_quality] end
Multiplication factor to average coverage to calculate maximum read coverage at the variant position to be considered for analysis @return [Integer]
# File lib/cheripic/options.rb, line 74 def self.max_d_multiple @user_settings[:max_d_multiple] end
Maximum read coverage at the variant position to be considered for analysis @return [Integer]
# File lib/cheripic/options.rb, line 60 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
# File lib/cheripic/options.rb, line 67 def self.maxdepth=(value) @user_settings[:maxdepth] = value end
Minimum reads supporting an indel at the variant position to be considered for analysis as indel @return [Integer]
# File lib/cheripic/options.rb, line 86 def self.min_indel_count_support @user_settings[:min_indel_count_support] end
Minimum non reference count at the variant position to be considered for analysis @return [Integer]
# File lib/cheripic/options.rb, line 80 def self.min_non_ref_count @user_settings[:min_non_ref_count] end
Minimum read coverage at the variant position to be considered for analysis @return [Integer]
# File lib/cheripic/options.rb, line 54 def self.mindepth @user_settings[:mindepth] end
Threshold for fraction of read bases at variant position below which are ignored as noise @return [Float]
# File lib/cheripic/options.rb, line 111 def self.noise @user_settings[:noise] end
Option to whether to set the input data is from polyploid or not @return [Boolean]
# File lib/cheripic/options.rb, line 136 def self.polyploidy @user_settings[:polyploidy] end
Number of nucleotides of sequence to select from each side of the selected variant @return [Integer]
# File lib/cheripic/options.rb, line 148 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
# File lib/cheripic/options.rb, line 154 def self.update(newset) @user_settings = @def_settings.merge(newset) end
Option to whether to ignore or consider the contigs with out any variants @return [Boolean]
# File lib/cheripic/options.rb, line 124 def self.use_all_contigs @user_settings[:use_all_contigs] end