betteridiot/bamnostic

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Do not use bare 'except'
Open

    except:
Severity: Minor
Found in bamnostic/utils.py by pep8

When catching exceptions, mention specific exceptions when possible.

Okay: except Exception:
Okay: except BaseException:
E722: except:

Missing whitespace after ','
Open

                self.__setitem__(k,v)
Severity: Minor
Found in bamnostic/utils.py by pep8

Each comma, semicolon or colon should be followed by whitespace.

Okay: [a, b]
Okay: (3,)
Okay: a[1:4]
Okay: a[:4]
Okay: a[1:]
Okay: a[1:4:2]
E231: ['a','b']
E231: foo(bar,baz)
E231: [{'a':'b'}]

Unexpected spaces around keyword / parameter equals
Open

def cigar_alignment(seq=None, cigar=None, start_pos = 0, qualities=None, base_qual_thresh=0, query=False):
Severity: Minor
Found in bamnostic/utils.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Do not use bare 'except'
Open

                except:
Severity: Minor
Found in bamnostic/bam.py by pep8

When catching exceptions, mention specific exceptions when possible.

Okay: except Exception:
Okay: except BaseException:
E722: except:

Ambiguous variable name 'l'
Open

                    l = int(part[3:])
Severity: Minor
Found in bamnostic/bam.py by pep8

Never use the characters 'l', 'O', or 'I' as variable names.

In some fonts, these characters are indistinguishable from the
numerals one and zero. When tempted to use 'l', use 'L' instead.

Okay: L = 0
Okay: o = 123
Okay: i = 42
E741: l = 0
E741: O = 123
E741: I = 42

Variables can be bound in several other contexts, including class
and function definitions, 'global' and 'nonlocal' statements,
exception handlers, and 'with' and 'for' statements.
In addition, we have a special handling for function parameters.

Okay: except AttributeError as o:
Okay: with lock as L:
Okay: foo(l=12)
Okay: for a in foo(l=12):
E741: except AttributeError as O:
E741: with lock as l:
E741: global I
E741: nonlocal l
E741: def foo(l):
E741: def foo(l=12):
E741: l = foo(l=12)
E741: for l in range(10):
E742: class I(object):
E743: def l(x):

Unexpected spaces around keyword / parameter equals
Open

    def __init__(self, filepath_or_object, mode = 'xb', compresslevel = 6, ignore_overwrite = False,
Severity: Minor
Found in bamnostic/bam.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Continuation line under-indented for visual indent
Open

                    'duplicate_filehandle': locals()['duplicate_filehandle']}
Severity: Minor
Found in bamnostic/bam.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)

Unexpected spaces around keyword / parameter equals
Open

def _cross_check_header_refs(reads, header="", referencenames = None, referencelengths = None):
Severity: Minor
Found in bamnostic/bam.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Unexpected spaces around keyword / parameter equals
Open

                copy_header = None, header = b'', reference_names = None, reference_lengths = None):
Severity: Minor
Found in bamnostic/bam.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Unexpected spaces around keyword / parameter equals
Open

def _cross_check_header_refs(reads, header="", referencenames = None, referencelengths = None):
Severity: Minor
Found in bamnostic/bam.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Unexpected spaces around keyword / parameter equals
Open

    def __init__(self, filepath_or_object, mode = 'xb', compresslevel = 6, ignore_overwrite = False,
Severity: Minor
Found in bamnostic/bam.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Unexpected spaces around keyword / parameter equals
Open

    def __init__(self, filepath_or_object, mode = 'xb', compresslevel = 6, ignore_overwrite = False,
Severity: Minor
Found in bamnostic/bam.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Unexpected spaces around keyword / parameter equals
Open

                copy_header = None, header = b'', reference_names = None, reference_lengths = None):
Severity: Minor
Found in bamnostic/bam.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Unexpected spaces around keyword / parameter equals
Open

                copy_header = None, header = b'', reference_names = None, reference_lengths = None):
Severity: Minor
Found in bamnostic/bam.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Unexpected spaces around keyword / parameter equals
Open

                copy_header = None, header = b'', reference_names = None, reference_lengths = None):
Severity: Minor
Found in bamnostic/bam.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Unexpected spaces around keyword / parameter equals
Open

                        reference_names = reference_names, 
Severity: Minor
Found in bamnostic/bam.py by pep8

Don't use spaces around the '=' sign in function arguments.

Don't use spaces around the '=' sign when used to indicate a
keyword argument or a default parameter value, except when
using a type annotation.

Okay: def complex(real, imag=0.0):
Okay: return magic(r=real, i=imag)
Okay: boolean(a == b)
Okay: boolean(a != b)
Okay: boolean(a <= b)
Okay: boolean(a >= b)
Okay: def foo(arg: int = 42):
Okay: async def foo(arg: int = 42):

E251: def complex(real, imag = 0.0):
E251: return magic(r = real, i = imag)
E252: def complex(real, image: float=0.0):

Continuation line under-indented for visual indent
Open

                                                        reference_names,
Severity: Minor
Found in bamnostic/bam.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)

Line break after binary operator
Open

            hash(self.pos) ^
Severity: Minor
Found in bamnostic/core.py by pep8

Avoid breaks after binary operators.

The preferred place to break around a binary operator is before the
operator, not after it.

W504: (width == 0 +\n height == 0)
W504: (width == 0 and\n height == 0)
W504: var = (1 &\n       ~2)

Okay: foo(\n    -x)
Okay: foo(x\n    [])
Okay: x = '''\n''' + ''
Okay: x = '' + '''\n'''
Okay: foo(x,\n    -y)
Okay: foo(x,  # comment\n    -y)

The following should be W504 but unary_context is tricky with these
Okay: var = (1 /\n       -2)
Okay: var = (1 +\n       -1 +\n       -2)

Blank line contains whitespace
Open

        
Severity: Minor
Found in bamnostic/csi.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
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