Showing 23 of 23 total issues
Method get_allele_depth has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def self.get_allele_depth(vcf_obj)
# check if the vcf is from samtools (has DP4 and AF1 fields in INFO)
if vcf_obj.info.key?('DP4')
freq = vcf_obj.info['DP4'].split(',')
ref = freq[0].to_f + freq[1].to_f- 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"