Showing 74 of 132 total issues
Method copy_raw_seq_files has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def copy_raw_seq_files(prev_tmp_dir)
return if @opt[:raw_sequences]
return unless @opt[:validations].include?('align') ||
@opt[:validations].include?('dup')
prev_raw_seq = Dir[File.join(prev_tmp_dir, '*raw_seq')]- 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
Method unimodality_test has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def unimodality_test(xx, yy)
mean_x = xx.mean
median_x = xx.median
mode_x = xx.mode
sd_x = xx.standard_deviation- 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
Method check_validations_output has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def check_validations_output(vals)
raise NoValidationError if @run_output.validations.empty?
vals.each do |v|
raise ReportClassError unless v.validation_report.is_a? ValidationReport
end- 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
Method validation has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def validation
# chack if there are different reading frames
count_p = 0
count_n = 0
frames.each do |x, _y|- 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
Method create_validation_hash has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def create_validation_hash(row)
row[:validations] = {}
@validations.each do |item|
val = add_basic_validation_info(item)
explain = add_explanation_data(item) if item.color != 'warning'- 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
Method write_an_index_file has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def write_an_index_file(output_file, db_type)
file = File.open(output_file, 'w+')
iterate_xml(file, db_type) if opt[:blast_xml_file]
iterate_tabular(file, db_type) if opt[:blast_tabular_file]
rescue BLASTDBError- 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
Method run has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def run
raise unless prediction.is_a?(Query)
start = Time.now
- 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
Method length_validation_scores has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def length_validation_scores(validations, scores)
lcv = validations.select { |v| v.class == LengthClusterValidationOutput }
lrv = validations.select { |v| v.class == LengthRankValidationOutput }
if lcv.length == 1 && lrv.length == 1
score_lcv = (lcv[0].result == lcv[0].expected)- 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
Method write_csv has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def write_csv
return unless @opt[:output_formats].include? 'csv'
File.open(@dirs[:csv_file], 'a') do |file|
file.puts csv_header.join(',')
@json_data.each do |data|- 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
Method remove_isolated_residues has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def remove_isolated_residues(seq, len = 2)
gap_starts = seq.to_enum(:scan, /(-\w{1,#{len}}-)/i).map { |_m| $`.size + 1 }
# remove isolated residues
gap_starts.each do |i|
(i..i + len - 1).each { |j| seq[j] = '-' if isalpha(seq[j]) }- 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
Method iterate_tabular has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def iterate_tabular(file, db_type)
table_headers = opt[:blast_tabular_options].split(/[ ,]/)
tab_file = File.read(opt[:blast_tabular_file])
rows = CSV.parse(tab_file, col_sep: "\t",
skip_lines: /^#/,- 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
Method extract_from_local_db has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def extract_from_local_db(batch, accno = nil, idx_file = nil)
efile = Tempfile.new('blast_out')
cmd = batch ? batch_raw_seq_cmd(idx_file) : single_raw_seq_cmd(accno, efile.path)
`#{cmd}`
raw_seqs = batch ? File.read(opt[:raw_sequences]) : efile.read- 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
Method run has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def run
if type.to_s != 'nucleotide'
@validation_report = ValidationReport.new('', :unapplicable)
return @validation_report
end- 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
Method run_blast_on_input_file has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def run_blast_on_input_file
remote = opt[:db].match?(/remote/) ? true : false
print_blast_info_text(remote)
log_file = File.join(dirs[:tmp_dir], 'blast_cmd_output.txt')- 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"