Showing 23 of 23 total issues
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 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)- 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 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- 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"