Showing 23 of 23 total issues
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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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 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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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
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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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
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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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 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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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 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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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 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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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 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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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 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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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 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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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 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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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 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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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 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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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"