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

base_quality() click to toggle source

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
bfr_adjust() click to toggle source

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
cross_type() click to toggle source

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
current_values() click to toggle source

Resets the values of options to defaults

# File lib/cheripic/options.rb, line 164
def self.current_values
  @user_settings
end
defaults() click to toggle source

Resets the values of options to defaults

# File lib/cheripic/options.rb, line 159
def self.defaults
  @user_settings = @def_settings
end
hmes_adjust() click to toggle source

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
hthigh() click to toggle source

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
htlow() click to toggle source

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
ignore_reference_n() click to toggle source

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
include_low_hmes() click to toggle source

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
mapping_quality() click to toggle source

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
max_d_multiple() click to toggle source

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
maxdepth() click to toggle source

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
maxdepth=(value) click to toggle source

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
min_indel_count_support() click to toggle source

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
min_non_ref_count() click to toggle source

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
mindepth() click to toggle source

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
noise() click to toggle source

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
polyploidy() click to toggle source

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
sel_seq_len() click to toggle source

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
update(newset) click to toggle source

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
use_all_contigs() click to toggle source

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