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TimothyStiles/poly

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io/gff/gff.go

Summary

Maintainability
A
0 mins
Test Coverage

Function Parse has 72 lines of code (exceeds 50 allowed). Consider refactoring.
Wontfix

func Parse(file io.Reader) (Gff, error) {
    fileBytes, err := readAllFn(file)
    if err != nil {
        return Gff{}, err
    }
Severity: Minor
Found in io/gff/gff.go - About 1 hr to fix

    Function Build has 63 lines of code (exceeds 50 allowed). Consider refactoring.
    Wontfix

    func Build(sequence Gff) ([]byte, error) {
    var gffBuffer bytes.Buffer

    versionString := "##gff-version 3 \n"
    if sequence.Meta.Version != "" {
    Severity: Minor
    Found in io/gff/gff.go - About 1 hr to fix

      Function Parse has a Cognitive Complexity of 25 (exceeds 20 allowed). Consider refactoring.
      Wontfix

      func Parse(file io.Reader) (Gff, error) {
    fileBytes, err := readAllFn(file)
    if err != nil {
        return Gff{}, err
    }
      Severity: Minor
      Found in io/gff/gff.go - About 1 hr 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 Parse has 7 return statements (exceeds 4 allowed).
      Wontfix

      func Parse(file io.Reader) (Gff, error) {
    fileBytes, err := readAllFn(file)
    if err != nil {
        return Gff{}, err
    }
      Severity: Major
      Found in io/gff/gff.go - About 45 mins to fix

        Avoid deeply nested control flow statements.
        Wontfix

                } else if fastaFlag && line[0:1] == ">" {
            gff.Meta.Description = line
        } else {
            record := Feature{}
            fields := strings.Split(line, "\t")
        Severity: Major
        Found in io/gff/gff.go - About 45 mins to fix

          Identical blocks of code found in 2 locations. Consider refactoring.
          Wontfix

          func getFeatureSequence(feature Feature, location Location) (string, error) {
    var sequenceBuffer bytes.Buffer
    var sequenceString string
    parentSequence := feature.ParentSequence.Sequence
          Severity: Major
          Found in io/gff/gff.go and 1 other location - About 2 hrs to fix
          io/genbank/genbank.go on lines 126..151

          Duplicated Code

          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

          Tuning

          This issue has a mass of 198.

          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

          Refactorings

          Further Reading

          Your code does not pass gofmt in 1 place. Go fmt your code!
          Open

          /*
          Severity: Minor
          Found in io/gff/gff.go by gofmt

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