Method argument_parser has 100 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def argument_parser
      cmds = self
      Trollop::Parser.new do
        version Cheripic::VERSION
        banner cmds.help_message

Method verify_bg_bulk_pileup has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

    def verify_bg_bulk_pileup
      unless defined?(@hmes_frags)
        self.hmes_frags
      end
      @hmes_frags.each_key do | frag |

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Method check_input_files has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

    def check_input_files(inputfiles)
      inputfiles.each_key do | type |
        inputfiles[type].flatten!
        check = 0
        inputfiles[type].each do | symbol |

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File variants.rb has 283 lines of code (exceeds 250 allowed). Consider refactoring.

Open

require 'bio'
require 'forwardable'

module Cheripic

Class Options has 22 methods (exceeds 20 allowed). Consider refactoring.

Open

  class Options

    # Default parameter settings
    @def_settings = {
        :hmes_adjust => 0.5,

Method bulks_compared has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

Open

    def bulks_compared
      @mut_bulk.each_key do | pos |
        ignore = 0
        unless @masked_regions.empty?
          @masked_regions.each_key do | index |

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File cmd.rb has 260 lines of code (exceeds 250 allowed). Consider refactoring.

Open

module Cheripic

  # A command line option and processing object to handle input options
  #
  # @!attribute [rw] options

Method get_bfr has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def self.get_bfr(mut_hash, bg_hash='')
      @bfr_adj = Options.bfr_adjust
      if bg_hash != ''
        # checking if only two vars in base hash and that includes ref
        # checking if only one var in hemi snp

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Method extract_bam_pileup has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

    def extract_bam_pileup(bamfile, sym)
      bq = Options.base_quality
      mq = Options.mapping_quality
      bamobject = Bio::DB::Sam.new(:bam=>bamfile, :fasta=>@params.assembly)
      bamobject.index unless bamobject.indexed?

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Method initialize has 35 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def initialize(inputs)
      set1 = %i{assembly
                input_format
                mut_bulk
                bg_bulk

Method check_input_files has 30 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def check_input_files(inputfiles)
      inputfiles.each_key do | type |
        inputfiles[type].flatten!
        check = 0
        inputfiles[type].each do | symbol |

Method set_max_depth has 29 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def set_max_depth(bamobject, bamfile)
      logger.info "processing #{bamfile} file for depth"
      all_depths = []
      bq = Options.base_quality
      mq = Options.mapping_quality

Method get_vars has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def self.get_vars(vcf_file)
      ht_low = Options.htlow
      ht_high = Options.hthigh

      # hash of :het and :hom with frag ids and respective variant positions

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Method select_contigs has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

Open

    def select_contigs(ratio_type)
      selected_contigs ={}
      use_all_contigs = Options.use_all_contigs
      @assembly.each_key do | frag |
        if use_all_contigs

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Method calculate_bfr has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def self.calculate_bfr(two_key_hash, other_hash)
      # if :ref is absent such as below noise depth, then set to zero
      unless two_key_hash.key?(:ref)
        two_key_hash[:ref] = 0
      end

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Method compare_pileups has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def compare_pileups
      unless @pileups_analyzed
        self.analyse_pileups
      end
      @assembly.each_key do | id |

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Method analyse_pileups has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def analyse_pileups
      if @params.input_format == 'bam'
        @vcf_hash = Vcf.filtering(@params.mut_bulk_vcf, @params.bg_bulk_vcf)
      end
      %i{mut_bulk bg_bulk mut_parent bg_parent}.each do | input |

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Method convert_boolean_strings has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def convert_boolean_strings
      %i{ambiguous_ref_bases use_all_contigs include_low_hmes polyploidy}.each do | symbol |
        if @options.key?(symbol)
          @options[symbol] = @options[symbol] == 'false' ? false : true
        end

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Method hemisnps_in_parent has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def hemisnps_in_parent
      # mark all the hemi snp based on both parents
      @mut_parent.each_key do |pos|
        mut_parent_frac = @mut_parent[pos].var_base_frac
        if @bg_parent.key?(pos)

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Method extract_vcfs has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

Open

    def extract_vcfs(vcffile, sym)
      # read vcf file and process each variant
      File.foreach(vcffile) do |line|
        next if line =~ /^#/
        v = Bio::DB::Vcf.new(line)

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