Function _tagger
has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring. Open
def _tagger(self):
"""Processes the variety of tags that accompany sequencing reads
The BAM format does not store the length of string and hex-formatted byte
arrays. These are null-terminated. Due to this, when parsing the byte stream,
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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=128,
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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 get_cigar_stats
has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring. Open
def get_cigar_stats(self):
"""Gets the counts of each CIGAR operation in the read and number of
nucleotides related to those given operations.
Returns:
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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 9 (exceeds 5 allowed). Consider refactoring. Open
def __init__(self, _io):
"""Instantiating the read parser just needs access to the BGZF io.object
Args:
io (BgzfReader): parser for processing BGZF files
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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 _range_popper
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def _range_popper(self, interval_start, interval_stop=None, front=True):
"""Simple pop method that accepts a range instead of a single value. Modifies the original bytearray by removing items
Note:
Pops from the front of the list by default. If `front` is set to `False`, it
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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
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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 _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
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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
Invalid escape sequence '\l' Open
mapq (int): :math:`-10\log_{10}P` mapping quality of read.
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- Exclude checks
Invalid escape sequences are deprecated in Python 3.6.
Okay: regex = r'\.png$'
W605: regex = '\.png$'
Line break after binary operator Open
hash(self.read_name) ^
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- Exclude checks
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)
Line break after binary operator Open
self.__class__ == other.__class__ and
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- Exclude checks
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)
Line break after binary operator Open
hash(self.reference_name) ^
- Read upRead up
- Exclude checks
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)
Unexpected spaces around keyword / parameter equals Open
with bam.BamWriter(bam_file, mode = 'ab') as bam_out:
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- Exclude checks
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):
Invalid escape sequence '\l' Open
score (:math:`Q`) is defined as :math:`Q=-10\log_{10}P`, where :math:`P`
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- Exclude checks
Invalid escape sequences are deprecated in Python 3.6.
Okay: regex = r'\.png$'
W605: regex = '\.png$'
Unexpected spaces around keyword / parameter equals Open
with bam.BamWriter(bam_file, mode = 'ab') as bam_out:
- Read upRead up
- Exclude checks
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):
Line break after binary operator Open
hash(self.pos) ^
- Read upRead up
- Exclude checks
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)