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Blahah/transrate

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lib/transrate/cmdline.rb

Summary

Maintainability
D
2 days
Test Coverage

File cmdline.rb has 478 lines of code (exceeds 250 allowed). Consider refactoring.
Open

module Transrate

class Cmdline

  require 'trollop'
Severity: Minor
Found in lib/transrate/cmdline.rb - About 7 hrs to fix

    Class Cmdline has 32 methods (exceeds 20 allowed). Consider refactoring.
    Open

    class Cmdline

  require 'trollop'
  require 'csv'
  require 'bindeps'
    Severity: Minor
    Found in lib/transrate/cmdline.rb - About 4 hrs to fix

      Method write_contig_csv has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
      Open

        def write_contig_csv a
    # write contig metrics to file for each contig
    outfile = File.expand_path "contigs.csv"
    logger.info "Writing contig metrics for each contig to #{outfile}"
    # have option to turn off, default on
      Severity: Minor
      Found in lib/transrate/cmdline.rb - About 1 hr to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

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

        def argument_parser
    cmdline = self
    Trollop::Parser.new do
      version Transrate::VERSION::STRING.dup
      banner cmdline.help_message
      Severity: Minor
      Found in lib/transrate/cmdline.rb - About 1 hr to fix

        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
        Severity: Minor
        Found in lib/transrate/cmdline.rb - About 1 hr to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        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|
        Severity: Minor
        Found in lib/transrate/cmdline.rb - About 1 hr to fix

          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}"
          Severity: Minor
          Found in lib/transrate/cmdline.rb - About 1 hr to fix

            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')
            Severity: Minor
            Found in lib/transrate/cmdline.rb - About 55 mins to fix

            Cognitive Complexity

            Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

            A method's cognitive complexity is based on a few simple rules:

            • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
            • Code is considered more complex for each "break in the linear flow of the code"
            • Code is considered more complex when "flow breaking structures are nested"

            Further reading

            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)
            Severity: Minor
            Found in lib/transrate/cmdline.rb - About 35 mins to fix

              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(',')
              Severity: Minor
              Found in lib/transrate/cmdline.rb - About 25 mins to fix

              Cognitive Complexity

              Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

              A method's cognitive complexity is based on a few simple rules:

              • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
              • Code is considered more complex for each "break in the linear flow of the code"
              • Code is considered more complex when "flow breaking structures are nested"

              Further reading

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