betteridiot/bamnostic

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bamnostic/bgzf.py

Summary

Maintainability
B
5 hrs
Test Coverage

Function read has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
Open

    def read(self, size=-1):
        """Read method for the BGZF module.

        Args:
            size (int): the number of bytes to read from file. Advances the cursor.
Severity: Minor
Found in bamnostic/bgzf.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 12 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(self, filepath_or_object, mode="rb", max_cache=None, 
                filename=None, duplicate_filehandle=None, ignore_truncation=False):
        """Initialize the class.

        Args:
Severity: Minor
Found in bamnostic/bgzf.py - 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 _load_block has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

    def _load_block(self, start_offset=None):
        """(PRIVATE) Used to load next BGZF block into the buffer, and orients the cursor position.

        Args:
            start_offset (int): byte offset of BGZF block (default: None)
Severity: Minor
Found in bamnostic/bgzf.py - 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

Avoid too many return statements within this function.
Open

                return data
Severity: Major
Found in bamnostic/bgzf.py - About 30 mins to fix

    Trailing whitespace
    Open

        def __init__(self, filepath_or_object, mode="rb", max_cache=None, 
    Severity: Minor
    Found in bamnostic/bgzf.py by pep8

    Trailing whitespace is superfluous.

    The warning returned varies on whether the line itself is blank,
    for easier filtering for those who want to indent their blank lines.
    
    Okay: spam(1)\n#
    W291: spam(1) \n#
    W293: class Foo(object):\n    \n    bang = 12

    Whitespace before ','
    Open

            FLG == 4 ,
    Severity: Minor
    Found in bamnostic/bgzf.py by pep8

    Avoid extraneous whitespace.

    Avoid extraneous whitespace in these situations:
    - Immediately inside parentheses, brackets or braces.
    - Immediately before a comma, semicolon, or colon.
    
    Okay: spam(ham[1], {eggs: 2})
    E201: spam( ham[1], {eggs: 2})
    E201: spam(ham[ 1], {eggs: 2})
    E201: spam(ham[1], { eggs: 2})
    E202: spam(ham[1], {eggs: 2} )
    E202: spam(ham[1 ], {eggs: 2})
    E202: spam(ham[1], {eggs: 2 })
    
    E203: if x == 4: print x, y; x, y = y , x
    E203: if x == 4: print x, y ; x, y = y, x
    E203: if x == 4 : print x, y; x, y = y, x

    At least two spaces before inline comment
    Open

            handle = handle._handle.name # get the raw file object, not wrapper
    Severity: Minor
    Found in bamnostic/bgzf.py by pep8

    Separate inline comments by at least two spaces.

    An inline comment is a comment on the same line as a statement.
    Inline comments should be separated by at least two spaces from the
    statement. They should start with a # and a single space.
    
    Each line of a block comment starts with a # and a single space
    (unless it is indented text inside the comment).
    
    Okay: x = x + 1  # Increment x
    Okay: x = x + 1    # Increment x
    Okay: # Block comment
    E261: x = x + 1 # Increment x
    E262: x = x + 1  #Increment x
    E262: x = x + 1  #  Increment x
    E265: #Block comment
    E266: ### Block comment

    Continuation line under-indented for visual indent
    Open

                    filename=None, duplicate_filehandle=None, ignore_truncation=False):
    Severity: Minor
    Found in bamnostic/bgzf.py by pep8

    Continuation lines indentation.

    Continuation lines should align wrapped elements either vertically
    using Python's implicit line joining inside parentheses, brackets
    and braces, or using a hanging indent.
    
    When using a hanging indent these considerations should be applied:
    - there should be no arguments on the first line, and
    - further indentation should be used to clearly distinguish itself
      as a continuation line.
    
    Okay: a = (\n)
    E123: a = (\n    )
    
    Okay: a = (\n    42)
    E121: a = (\n   42)
    E122: a = (\n42)
    E123: a = (\n    42\n    )
    E124: a = (24,\n     42\n)
    E125: if (\n    b):\n    pass
    E126: a = (\n        42)
    E127: a = (24,\n      42)
    E128: a = (24,\n    42)
    E129: if (a or\n    b):\n    pass
    E131: a = (\n    42\n 24)

    Closing bracket does not match indentation of opening bracket's line
    Open

            ]
    Severity: Minor
    Found in bamnostic/bgzf.py by pep8

    Continuation lines indentation.

    Continuation lines should align wrapped elements either vertically
    using Python's implicit line joining inside parentheses, brackets
    and braces, or using a hanging indent.
    
    When using a hanging indent these considerations should be applied:
    - there should be no arguments on the first line, and
    - further indentation should be used to clearly distinguish itself
      as a continuation line.
    
    Okay: a = (\n)
    E123: a = (\n    )
    
    Okay: a = (\n    42)
    E121: a = (\n   42)
    E122: a = (\n42)
    E123: a = (\n    42\n    )
    E124: a = (24,\n     42\n)
    E125: if (\n    b):\n    pass
    E126: a = (\n        42)
    E127: a = (24,\n      42)
    E128: a = (24,\n    42)
    E129: if (a or\n    b):\n    pass
    E131: a = (\n    42\n 24)

    There are no issues that match your filters.

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