betteridiot/bamnostic

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

    def _qual_builder(self):
        """Pulls out the quality information for the given read

        Attributes:
            query_qualities (:py:obj:`array.array`): Array of Phred quality scores for each base
Severity: Minor
Found in bamnostic/core.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

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

    def cull(self):
        """ Main utility function for pruning the LruDict

        If the length of the LruDict is more than `max_cache`, it removes the LRU item
        """
Severity: Minor
Found in bamnostic/utils.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

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

    def _check_sq(self):
        """ Inspect BAM file for @SQ entries within the header

        The implementation of this check is for BAM files specifically. I inspects
        the SAM header (if present) for the `@SQ` entires. However, if the SAM header
Severity: Minor
Found in bamnostic/bam.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

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

    def __init__(self, *args, **kwargs):
        """ Initialize the dictionary based on collections.OrderedDict. This
        is built of the basic `OrderedDict`. The major difference in instantiation
        is the usage of the `max_cache` argument. This sets the dictionary size
        to be used.
Severity: Minor
Found in bamnostic/utils.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

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

    def to_bam(bam_file):
        """Writes the alignment record to a BAM file

        Args:
            bam_file (string or :py:obj:`bamnostic.bam.BamWriter`): BAM file path or open bam file in a write mode
Severity: Minor
Found in bamnostic/core.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

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

    def __init__(self, filename):
        """Initialization method

        Generates an "index" of the index. This gives us the byte positions of each chromosome
        within the index file. Now, when a user queries over a specific chromosome, it pulls
Severity: Minor
Found in bamnostic/csi.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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