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vanheeringen-lab/peaksql

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Showing 10 of 10 total issues

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

def _nuc_to_onehot_idx(nuc: int) -> int:
    """
    Convert a nucleotide to a one hot index, where the indexes 0, 1, 2, 3 respectively
    correspond to A, C, G, T.
Severity: Minor
Found in peaksql/util.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 _add_bigwig has 5 arguments (exceeds 4 allowed). Consider refactoring.
Open

    def _add_bigwig(self, data_path, assembly_id, condition_id, extension):
Severity: Minor
Found in peaksql/database.py - About 35 mins to fix

    Function get_label has 5 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def get_label(
    Severity: Minor
    Found in peaksql/datasets/bed.py - About 35 mins to fix

      Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(
      Severity: Minor
      Found in peaksql/datasets/narrowpeak.py - About 35 mins to fix

        Function array_from_query has 5 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def array_from_query(
        Severity: Minor
        Found in peaksql/datasets/bed.py - About 35 mins to fix

          Function _add_bed has 5 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def _add_bed(self, data_path, assembly_id, condition_id, extension):
          Severity: Minor
          Found in peaksql/database.py - About 35 mins to fix

            Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def __init__(
            Severity: Minor
            Found in peaksql/datasets/bedregion.py - About 35 mins to fix

              Function binary_search has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
              Open

              def binary_search(index: int, lens: np.ndarray) -> int:
    """
    Does a binary search to not find the value in a list, but the index where the value
    is in between two values (returns the higher index of the two).
              Severity: Minor
              Found in peaksql/util.py - About 35 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 np.random.choice(idx)
              Severity: Major
              Found in peaksql/util.py - About 30 mins to fix

                Function array_from_query has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                Open

                    def array_from_query(
        self,
        query: List[Tuple[int, int, int, int]],
        cur_chrom_id: int,
        chromstart: int,
                Severity: Minor
                Found in peaksql/datasets/narrowpeak.py - About 25 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

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