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Showing 5 of 5 total issues

Function run_filters has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
Open

def run_filters( vdat, filtering = None ):
    """ 
    vdat - dictionary of INFO field from VCF line
    filtering - dictionary of fields to be filtered; defaults to None
    Currently implemented for sensitive and specific. Can modify the
Severity: Minor
Found in utils/classify_WHAM_vcf.py - About 2 hrs to fix

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

Function __init__ has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self,file):
        self.f = open(file,'r')
        #proces all of the header lines of the vcf. 
        header = True #boolean to continye looping through header
        info_boolean = False #need a boolean to trigger and append new INFO fields
Severity: Minor
Found in utils/classify_WHAM_vcf.py - About 45 mins to fix

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

Avoid too many return statements within this function.
Open

            return( pass_filt )
Severity: Major
Found in utils/classify_WHAM_vcf.py - About 30 mins to fix

    Avoid too many return statements within this function.
    Open

                return( pass_filt )
    Severity: Major
    Found in utils/classify_WHAM_vcf.py - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

                  return( pass_filt )
      Severity: Major
      Found in utils/classify_WHAM_vcf.py - About 30 mins to fix
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