Showing 46 of 167 total issues
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- Read upRead up
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
"""- Read upRead up
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- Read upRead up
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.- Read upRead up
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- Read upRead up
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- Read upRead up
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"