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

Open

module Transrate

class Cmdline

  require 'trollop'

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

Open

class Cmdline

  require 'trollop'
  require 'csv'
  require 'bindeps'

Method per_target_contig_reference_coverage has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.

Open

    def per_target_contig_reference_coverage crbblast
      # each target sequence in the reference can have multiple query contigs
      # hit it. to calculate the reference coverage you can't just add up the
      # alignment lengths. you have to make sure that overlaps are taken into
      # account

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Class Contig has 26 methods (exceeds 20 allowed). Consider refactoring.

Open

  class Contig

    include Enumerable
    extend Forwardable
    def_delegators :@seq, :size, :length

Method build_index has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.

Open

    def build_index file, threads
      @index_name = File.basename(file, File.extname(file))
      n = 4
      err = ""
      loop do

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Method basic_bin_stats has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def basic_bin_stats bin

      # cumulative length is a float so we can divide it
      # accurately later to get the mean length
      cumulative_length = 0.0

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Method per_target_contig_reference_coverage has 53 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def per_target_contig_reference_coverage crbblast
      # each target sequence in the reference can have multiple query contigs
      # hit it. to calculate the reference coverage you can't just add up the
      # alignment lengths. you have to make sure that overlaps are taken into
      # account

Method basic_bin_stats has 49 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def basic_bin_stats bin

      # cumulative length is a float so we can divide it
      # accurately later to get the mean length
      cumulative_length = 0.0

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

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Method per_query_contig_reference_coverage has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def per_query_contig_reference_coverage
      # for each query contig in the @assembly find out how much it covers
      # the reference
      n_refs_with_recip = 0
      total_crbb_hits = 0

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

Open

    def run left, right, threads:8
      # check all read files exist
      [left, right].each do |readfile|
        raise TransrateIOError.new "Read file is nil" if readfile.nil?
        readfile.split(",").each do |file|

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Method initialize has 35 lines of code (exceeds 25 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

Method map_reads has 32 lines of code (exceeds 25 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)

Method build_index has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def build_index file, threads
      @index_name = File.basename(file, File.extname(file))
      n = 4
      err = ""
      loop do

Method optimal_score has 32 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def optimal_score(prefix='assembly')
      return [@optimal, @cutoff] unless @optimal.nil?
      product = 0
      good = 0
      @assembly.assembly.each do |key, contig|

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

Method classify_contigs has 29 lines of code (exceeds 25 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|

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

Open

    def run left, right, threads:8
      # check all read files exist
      [left, right].each do |readfile|
        raise TransrateIOError.new "Read file is nil" if readfile.nil?
        readfile.split(",").each do |file|

Method per_query_contig_reference_coverage has 28 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def per_query_contig_reference_coverage
      # for each query contig in the @assembly find out how much it covers
      # the reference
      n_refs_with_recip = 0
      total_crbb_hits = 0

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

Open

    def get_read_length(left, right)
      count=0
      file = File.open(left.split(",").first)
      name = file.readline.chomp
      seq = file.readline.chomp

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