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Unexpected spaces around keyword / parameter equals
Open

                with bam.BamWriter(bam_file, mode = 'ab') as bam_out:
Severity: Minor
Found in bamnostic/core.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):

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

Trailing whitespace
Open

                    'filename': locals()['filename'], 'ignore_truncation': locals()['ignore_truncation'],
Severity: Minor
Found in bamnostic/bam.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

Missing whitespace around arithmetic operator
Open

                                cytosine[index - start if index-start > 0 else 0] += 1
Severity: Minor
Found in bamnostic/bam.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Ambiguous variable name 'l'
Open

            l = None
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):

Continuation line under-indented for visual indent
Open

                                                        reference_lengths)
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)

Trailing whitespace
Open

                if next_read.reference_name != query.contig:
Severity: Minor
Found in bamnostic/bam.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

Missing whitespace around arithmetic operator
Open

                                adenine[index - start if index-start > 0 else 0] += 1
Severity: Minor
Found in bamnostic/bam.py by pep8

Surround operators with a single space on either side.

- Always surround these binary operators with a single space on
  either side: assignment (=), augmented assignment (+=, -= etc.),
  comparisons (==, <, >, !=, <=, >=, in, not in, is, is not),
  Booleans (and, or, not).

- If operators with different priorities are used, consider adding
  whitespace around the operators with the lowest priorities.

Okay: i = i + 1
Okay: submitted += 1
Okay: x = x * 2 - 1
Okay: hypot2 = x * x + y * y
Okay: c = (a + b) * (a - b)
Okay: foo(bar, key='word', *args, **kwargs)
Okay: alpha[:-i]

E225: i=i+1
E225: submitted +=1
E225: x = x /2 - 1
E225: z = x **y
E225: z = 1and 1
E226: c = (a+b) * (a-b)
E226: hypot2 = x*x + y*y
E227: c = a|b
E228: msg = fmt%(errno, errmsg)

Continuation line under-indented for visual indent
Open

                copy_header = None, header = b'', reference_names = None, reference_lengths = None):
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 __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):

Blank line contains whitespace
Open
Severity: Minor
Found in bamnostic/bam.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

Unexpected spaces around keyword / parameter equals
Open

                super(BamWriter, self).__init__(filepath_or_object, mode=mode, compresslevel = compresslevel)
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 write_header(self, 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):

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)

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):

Blank line contains whitespace
Open
Severity: Minor
Found in bamnostic/bam.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

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):
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