Showing 165 of 167 total issues
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 query
has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring. Open
def query(self, ref_id, start, stop=-1):
""" Main query function for determining seek offset to BAM section that
AlignedRead objects from specified region start
Args:
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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 _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)
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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 _handle_split_region
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def _handle_split_region(split_roi, until_eof=False):
""" Checks format against `until_eof` and creates the Roi object
Args:
split_roi (:py:obj:`list` or :py::obj:`tuple`): the contig, start, and stop information.
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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, filepath_or_object, mode="rb", max_cache=128, index_filename=None,
filename=None, check_header=False, check_sq=True, reference_filename=None,
filepath_index=None, require_index=False, duplicate_filehandle=None,
ignore_truncation=False):
"""Initialize the class.
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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 mate
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def mate(self, AlignedSegment):
""" Gets the mate to a given AlignedSegment.
Note:
Slow, when compared to the C-API. Not meant for high-throughput analysis.
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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 get_ref
has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def get_ref(self, ref_id=None, idx=False):
"""Interatively unpacks all the bins, linear intervals, and chunks for a given reference
A reference is comprised of 2 things: 1) a series of bins that reference chunks of aligned
reads that are grouped within that bin. 2) a series of virtual offsets of the first read of a
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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_index
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def _init_index(self):
"""Initialize the index file (BAI)"""
if self._check_idx:
# self._index = bamnostic.bai.Bai(self._index_path)
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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
Avoid deeply nested control flow statements. Open
if len(split_field) > 2:
tag = split_field[0]
value = split_field[2]
else:
tag, value = split_field
Avoid deeply nested control flow statements. Open
if seg_qual[index] >= base_qual_thresh:
yield base, start_pos
else:
Function _cross_check_header_refs
has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring. Open
def _cross_check_header_refs(reads, header="", referencenames = None, referencelengths = None):
"""Modified code from Peter Cock's [BamWriter](https://github.com/peterjc/biopython/blob/SamBam2015/Bio/Sequencing/SamBam/__init__.py#L1714)
"""
if not header:
# If the reads argument is a SamIterator or BamIterator this works:
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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
Avoid deeply nested control flow statements. Open
if start <= index < stop:
if base == 'A':
adenine[index - start if index-start > 0 else 0] += 1
elif base == 'G':
guanine[index - start if index-start > 0 else 0] += 1
Avoid deeply nested control flow statements. Open
if qualities is not None:
if seg_qual[index] >= base_qual_thresh:
yield base, start_pos
else:
yield base, start_pos
Function get_ref
has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def get_ref(self, ref_id=None, idx=False):
"""Iteratively unpacks all the bins, linear intervals, and chunks for a given reference
A reference is comprised of 2 things: 1) a series of bins that reference chunks of aligned
reads that are grouped within that bin. 2) a series of virtual offsets of the first read of a
- 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
Identical blocks of code found in 2 locations. Consider refactoring. Open
self.ref_indices = {ref: self.get_ref(ref, idx=True) for ref in range(self.n_refs)}
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Duplicated Code
Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:
Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.
When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).
Tuning
This issue has a mass of 33.
We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.
The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.
If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.
See codeclimate-duplication
's documentation for more information about tuning the mass threshold in your .codeclimate.yml
.
Refactorings
- Extract Method
- Extract Class
- Form Template Method
- Introduce Null Object
- Pull Up Method
- Pull Up Field
- Substitute Algorithm
Further Reading
- Don't Repeat Yourself on the C2 Wiki
- Duplicated Code on SourceMaking
- Refactoring: Improving the Design of Existing Code by Martin Fowler. Duplicated Code, p76
Function md_changes
has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def md_changes(seq, md_tag):
"""Recreates the reference sequence of a given alignment to the extent that the
MD tag can represent.
Note:
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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 reg2bins
has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def reg2bins(rbeg, rend):
"""Generates bin ids which overlap the specified region.
Args:
rbeg (int): inclusive beginning position of region
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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 update
has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def update(self, others):
""" Same as a regular `dict.update`, however, since pypy's `dict.update`
doesn't go through `dict.__setitem__`, this is used to ensure it does
Args:
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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"