Showing 46 of 167 total issues
Function count_coverage
has a Cognitive Complexity of 55 (exceeds 5 allowed). Consider refactoring. Open
def count_coverage(self, contig=None, start=None, stop=None, region=None,
quality_threshold=15, read_callback='all',
reference=None, end=None, base_quality_threshold=0):
""" Counts the coverage of each base supported by a read the given interval.
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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 cigar_alignment
has a Cognitive Complexity of 50 (exceeds 5 allowed). Consider refactoring. Open
def cigar_alignment(seq=None, cigar=None, start_pos = 0, qualities=None, base_qual_thresh=0, query=False):
"""Use the CIGAR to filter out all unaligned data bases
Any clipping results in the removal of those bases. If an insertion is seen in
the CIGAR, those bases are removed from the sequence. If a deletion is seen in
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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 fetch
has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring. Open
def fetch(self, contig=None, start=None, stop=None, region=None,
tid=None, until_eof=False, multiple_iterators=False,
reference=None, end=None):
"""Creates a generator that returns all reads within the given region. (inclusive, exclusive)
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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 parse_region
has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring. Open
def parse_region(contig=None, start=None, stop=None, region=None,
tid=None, reference=None, end=None, until_eof=False):
r""" Parses region information from all user set parameters.
The main goal of this function is to handle the many different ways a user
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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 24 (exceeds 5 allowed). Consider refactoring. Open
def __init__(self, _io):
""" Initialize the header
Args:
_io (:py:obj:`file`): opened BAM file object
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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 read
has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring. Open
def read(self, size=-1):
"""Read method for the BGZF module.
Args:
size (int): the number of bytes to read from file. Advances the cursor.
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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 19 (exceeds 5 allowed). Consider refactoring. Open
def __init__(self, filepath_or_object, mode = 'xb', compresslevel = 6, ignore_overwrite = False,
copy_header = None, header = b'', reference_names = None, reference_lengths = None):
"""Useful class for writing BAM files.
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 check_index
has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring. Open
def check_index(self, index_filename=None, req_idx=False):
""" Checks to make sure index file is available. If not, it disables random access.
Args:
index_filename (str): path to index file (BAI) if it does not fit naming convention (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 _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 _sam_header_to_ref_list
has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring. Open
def _sam_header_to_ref_list(header):
"""Modified code from Peter Cock's [BamWriter](https://github.com/peterjc/biopython/blob/SamBam2015/Bio/Sequencing/SamBam/__init__.py#L1714)
Removes blank lines, ensures trailing newlines, spots some errors.
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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_bins
has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring. Open
def get_bins(self, n_bins, ref_id=None, idx=False):
"""Simple function that iteratively unpacks the data of a number (`n_bin`)
of bins.
As the function discovers the number of chunks needed for a given
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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_bins
has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring. Open
def get_bins(self, n_bins, ref_id=None, idx=False):
"""Simple function that iteratively unpacks the data of a number (`n_bin`)
of bins.
As the function discovers the number of chunks needed for a given
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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 write_header
has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring. Open
def write_header(self, copy_header = None, header = b'', reference_names = None, reference_lengths = None):
"""Modified code from Peter Cock's [BamWriter](https://github.com/peterjc/biopython/blob/SamBam2015/Bio/Sequencing/SamBam/__init__.py#L1714)
Writes the header into a BAM file
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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 12 (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 __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 __init__
has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring. Open
def __init__(self, filepath_or_object, mode="rb", max_cache=None,
filename=None, duplicate_filehandle=None, ignore_truncation=False):
"""Initialize the class.
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 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:
- 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 _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 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"