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

Open

  def check_reads
    if @opts.left and @opts.right
      if @opts.left.split(",").length != @opts.right.split(",").length
        msg = "Please provide the same number of left reads as right reads"
        raise TransrateArgError.new msg

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Method print_missing_dependencies has 27 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def print_missing_dependencies(missing, blast_missing)
    if missing.length + blast_missing.length > 0
      puts "Dependencies are missing:"

      missing.each do |dep|

Method analyse_assembly has 26 lines of code (exceeds 25 allowed). Consider refactoring.

Open

  def analyse_assembly(assembly, r, result_path)
    logger.info "Loading assembly: #{assembly}"
    a = Assembly.new assembly

    logger.info "Analysing assembly: #{assembly}"

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

Open

  def check_dependencies
    # Check dependencies if they are relevant to the command issued,
    # and handle any commands to install missing ones
    gem_dir = Gem.loaded_specs['transrate'].full_gem_path
    gem_deps = File.join(gem_dir, 'deps', 'deps.yaml')

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

Open

    def run assembly, bamfile, threads=8
      assembly = assembly.file if assembly.is_a? Assembly
      output = "quant.sf"
      sampled_bam = "postSample.bam"
      @fin_output = "#{File.basename assembly}_#{output}"

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

Open

    def initialize(assembly, reference, threads: 1)
      if assembly
        if assembly.is_a?(Assembly)
          @assembly = assembly
        else

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

Open

    def classify_contigs cutoff
      # create hash of file handles for each output
      base = File.basename @file
      files = {}
      %w(good bad).each do |type|

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

Open

    def initialize file
      @file = File.expand_path file
      unless File.exist? @file
        raise TransrateIOError.new "Assembly file doesn't exist: #{@file}"
      end

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Method install_missing_dependencies has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

  def install_missing_dependencies(deps, read_deps, ref_deps,
                                   gem_deps, blast_dep)

Method analyse_expression has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def analyse_expression salmon_output
      salmon_output.each_pair do |name, expr|
        contig_name = Bio::FastaDefline.new(name.to_s).entry_id
        contig_name.gsub!(/;$/, '') # trim trailing semicolon
        contig = @assembly[contig_name]

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Method map_reads has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def map_reads(file, left, right, outputname: nil, threads: 8)
      raise SnapError.new("Index not built") if !@index_built

      lbase = File.basename(left.split(",").first)
      rbase = File.basename(right.split(",").first)

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

Open

    def load_expression file
      expression = {}
      first = true
      File.open(file).each do |line|
        if first

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

Open

  def check_assembly
    if @opts.assembly
      @opts[:assembly] = @opts.assembly.split(',').map do |a|
        File.expand_path a
      end.join(',')

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

Open

    def load_readcount reads
      @read_count = 0
      if File.exist?("#{@read_count_file}")
        @read_count = File.open("#{@read_count_file}").readlines.join.to_i
      else

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