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 |- Read upRead up
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
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?- Read upRead up
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 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_qualityMethod 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- Read upRead up
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 |- Read upRead up
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 |- Read upRead up
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)- Read upRead up
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 a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def initialize(options)
@params = options
@assembly = {}
@pileups = {}
Bio::FastaFormat.open(@params.assembly).each do |entry|- Read upRead up
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 get_cutoff has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def get_cutoff(selected_contigs, ratio_type)
include_low_hmes = Options.include_low_hmes
# set minimum cut off hme_score or bfr_score to pick fragments with variants
# calculate min hme score for back or out crossed data or bfr_score for polypoidy data
# if no filtering applied set cutoff to 1.1- Read upRead up
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"