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wurmlab/GeneValidator

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lib/genevalidator/validation_duplication.rb

Summary

Maintainability
C
1 day
Test Coverage
B
84%

Method run has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.
Open

    def run(n = 10)
      raise NotEnoughHitsError if hits.length < opt[:min_blast_hits]
      raise unless prediction.is_a?(Query) && !prediction.raw_sequence.nil? &&
                   hits[0].is_a?(Query)
Severity: Minor
Found in lib/genevalidator/validation_duplication.rb - About 3 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

Method run has 70 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    def run(n = 10)
      raise NotEnoughHitsError if hits.length < opt[:min_blast_hits]
      raise unless prediction.is_a?(Query) && !prediction.raw_sequence.nil? &&
                   hits[0].is_a?(Query)
Severity: Major
Found in lib/genevalidator/validation_duplication.rb - About 2 hrs to fix

    Method check_multiple_coverage has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

        def check_multiple_coverage(hit_alignment, query_alignment, hsp, coverage,
                                ranges_prediction)
      # for each hsp of the curent hit
      # iterate through the alignment and count the matching residues
      [*(0..hit_alignment.length - 1)].each do |i|
    Severity: Minor
    Found in lib/genevalidator/validation_duplication.rb - About 55 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

    Method initialize has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def initialize(short_header, header, description, pvalue, averages,
                   threshold = 0.05, expected = :yes)
    Severity: Major
    Found in lib/genevalidator/validation_duplication.rb - About 50 mins to fix

      Method check_multiple_coverage has 5 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def check_multiple_coverage(hit_alignment, query_alignment, hsp, coverage,
                                ranges_prediction)
      Severity: Minor
      Found in lib/genevalidator/validation_duplication.rb - About 35 mins to fix

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