Class: Cheripic::Options

Inherits:
Object
  • Object
show all
Defined in:
lib/cheripic/options.rb

Overview

A class to get default settings and update user settings for parameters and facilitate retrieval of settings any where in the module

Class Method Summary collapse

Class Method Details

.base_quality ⇒ Integer

Minimum aligned base quality at the variant position to be considered for analysis

Returns:

  • (Integer) 


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# File 'lib/cheripic/options.rb', line 105

def self.base_quality
  @user_settings[:base_quality]
end

.bfr_adjust ⇒ Float

A value to adjust calculation of bulk frequency ratio (bfr)

Returns:

  • (Float) 


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# File 'lib/cheripic/options.rb', line 142

def self.bfr_adjust
  @user_settings[:bfr_adjust]
end

.cross_type ⇒ String

Note:

options are either ‘back’ or ‘out’

Option for cross type used for generating bulk population

Returns:

  • (String) 


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# File 'lib/cheripic/options.rb', line 118

def self.cross_type
  @user_settings[:cross_type]
end

.current_values ⇒ Object

Resets the values of options to defaults



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# File 'lib/cheripic/options.rb', line 164

def self.current_values
  @user_settings
end

.defaults ⇒ Object

Resets the values of options to defaults



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# File 'lib/cheripic/options.rb', line 159

def self.defaults
  @user_settings = @def_settings
end

.hmes_adjust ⇒ Float

A value to adjust calculation of Homozygosity Enrichment Score (HMES)

Returns:

  • (Float) 


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# File 'lib/cheripic/options.rb', line 36

def self.hmes_adjust
  @user_settings[:hmes_adjust]
end

.hthigh ⇒ Float

Higher cut off of Allele fraction for categorization of an variant to heterozygous

Returns:

  • (Float) 


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# File 'lib/cheripic/options.rb', line 48

def self.hthigh
  @user_settings[:hthigh]
end

.htlow ⇒ Float

Lower cut off of Allele fraction for categorization of an variant to heterozygous

Returns:

  • (Float) 


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# File 'lib/cheripic/options.rb', line 42

def self.htlow
  @user_settings[:htlow]
end

.ignore_reference_n ⇒ Boolean

Note:

switching option name here so Pileup options are same

Option to whether to ignore or consider the reference positions which are ambiguous

Returns:

  • (Boolean) 


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# File 'lib/cheripic/options.rb', line 93

def self.ignore_reference_n
  @user_settings[:ambiguous_ref_bases] ? false : true
end

.include_low_hmes ⇒ Boolean

Option to whether to ignore or consider the contigs with low HME score

Returns:

  • (Boolean) 


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# File 'lib/cheripic/options.rb', line 130

def self.include_low_hmes
  @user_settings[:include_low_hmes]
end

.mapping_quality ⇒ Integer

Minimum alignment mapping quality of the read to be used for bam files

Returns:

  • (Integer) 


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# File 'lib/cheripic/options.rb', line 99

def self.mapping_quality
  @user_settings[:mapping_quality]
end

.max_d_multiple ⇒ Integer

Multiplication factor to average coverage to calculate maximum read coverage at the variant position to be considered for analysis

Returns:

  • (Integer) 


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# File 'lib/cheripic/options.rb', line 74

def self.max_d_multiple
  @user_settings[:max_d_multiple]
end

.maxdepth ⇒ Integer

Maximum read coverage at the variant position to be considered for analysis

Returns:

  • (Integer) 


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# File 'lib/cheripic/options.rb', line 60

def self.maxdepth
  @user_settings[:maxdepth]
end

.maxdepth=(value) ⇒ Integer

Setting maximum read coverage at the variant position to be considered for analysis

Parameters:

  • value (Integer) —

    provided integer value will be updated as maxdepth

Returns:

  • (Integer) —

    updated maxdepth value



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# File 'lib/cheripic/options.rb', line 67

def self.maxdepth=(value)
  @user_settings[:maxdepth] = value
end

.min_indel_count_support ⇒ Integer

Minimum reads supporting an indel at the variant position to be considered for analysis as indel

Returns:

  • (Integer) 


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# File 'lib/cheripic/options.rb', line 86

def self.min_indel_count_support
  @user_settings[:min_indel_count_support]
end

.min_non_ref_count ⇒ Integer

Minimum non reference count at the variant position to be considered for analysis

Returns:

  • (Integer) 


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# File 'lib/cheripic/options.rb', line 80

def self.min_non_ref_count
  @user_settings[:min_non_ref_count]
end

.mindepth ⇒ Integer

Minimum read coverage at the variant position to be considered for analysis

Returns:

  • (Integer) 


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# File 'lib/cheripic/options.rb', line 54

def self.mindepth
  @user_settings[:mindepth]
end

.noise ⇒ Float

Threshold for fraction of read bases at variant position below which are ignored as noise

Returns:

  • (Float) 


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# File 'lib/cheripic/options.rb', line 111

def self.noise
  @user_settings[:noise]
end

.polyploidy ⇒ Boolean

Option to whether to set the input data is from polyploid or not

Returns:

  • (Boolean) 


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# File 'lib/cheripic/options.rb', line 136

def self.polyploidy
  @user_settings[:polyploidy]
end

.sel_seq_len ⇒ Integer

Number of nucleotides of sequence to select from each side of the selected variant

Returns:

  • (Integer) 


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# File 'lib/cheripic/options.rb', line 148

def self.sel_seq_len
  @user_settings[:sel_seq_len]
end

.update(newset) ⇒ Object

Updates the values of options using a hash generated from user inputs

Parameters:

  • newset (Hash) —

    a hash of option names as keys user settings as values



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# File 'lib/cheripic/options.rb', line 154

def self.update(newset)
  @user_settings = @def_settings.merge(newset)
end

.use_all_contigs ⇒ Boolean

Option to whether to ignore or consider the contigs with out any variants

Returns:

  • (Boolean) 


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# File 'lib/cheripic/options.rb', line 124

def self.use_all_contigs
  @user_settings[:use_all_contigs]
end