bio-miga/miga

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lib/miga/common/format.rb

Summary

Maintainability
C
1 day
Test Coverage
A
100%

Assignment Branch Condition size for seqs_length is too high. [96.04/15]
Open

  def seqs_length(file, format, opts = {})
    opts[:gc] = true if opts[:skew]
    fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
    l = []
    gc = 0
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Module has too many lines. [105/100]
Open

module MiGA::Common::Format
  ##
  # Tabulates an +values+, and Array of Arrays, all with the same number of
  # entries as +header+. Returns an Array of String, one per line.
  def tabulate(header, values, tabular = false)
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [50/10]
Open

  def seqs_length(file, format, opts = {})
    opts[:gc] = true if opts[:skew]
    fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
    l = []
    gc = 0
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [37/10]
Open

  def clean_fasta_file(file)
    tmp_fh = nil
    tmp_path = nil
    begin
      if file =~ /\.gz/
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method seqs_length has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
Open

  def seqs_length(file, format, opts = {})
    opts[:gc] = true if opts[:skew]
    fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
    l = []
    gc = 0
Severity: Minor
Found in lib/miga/common/format.rb - About 4 hrs to fix

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

Assignment Branch Condition size for clean_fasta_file is too high. [33.91/15]
Open

  def clean_fasta_file(file)
    tmp_fh = nil
    tmp_path = nil
    begin
      if file =~ /\.gz/
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Assignment Branch Condition size for tabulate is too high. [30.1/15]
Open

  def tabulate(header, values, tabular = false)
    fields = []
    fields << header.map(&:to_s) unless tabular && header.all?(&:nil?)
    fields << fields.first.map { |h| h.gsub(/\S/, '-') } unless tabular
    fields += values.map { |r| r.map { |cell| cell.nil? ? '?' : cell.to_s } }
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Cyclomatic complexity for seqs_length is too high. [19/6]
Open

  def seqs_length(file, format, opts = {})
    opts[:gc] = true if opts[:skew]
    fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
    l = []
    gc = 0
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Perceived complexity for seqs_length is too high. [20/7]
Open

  def seqs_length(file, format, opts = {})
    opts[:gc] = true if opts[:skew]
    fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
    l = []
    gc = 0
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Method tabulate has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
Open

  def tabulate(header, values, tabular = false)
    fields = []
    fields << header.map(&:to_s) unless tabular && header.all?(&:nil?)
    fields << fields.first.map { |h| h.gsub(/\S/, '-') } unless tabular
    fields += values.map { |r| r.map { |cell| cell.nil? ? '?' : cell.to_s } }
Severity: Minor
Found in lib/miga/common/format.rb - About 2 hrs to fix

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 seqs_length has 50 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def seqs_length(file, format, opts = {})
    opts[:gc] = true if opts[:skew]
    fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r')
    l = []
    gc = 0
Severity: Minor
Found in lib/miga/common/format.rb - About 2 hrs to fix

Cyclomatic complexity for tabulate is too high. [8/6]
Open

  def tabulate(header, values, tabular = false)
    fields = []
    fields << header.map(&:to_s) unless tabular && header.all?(&:nil?)
    fields << fields.first.map { |h| h.gsub(/\S/, '-') } unless tabular
    fields += values.map { |r| r.map { |cell| cell.nil? ? '?' : cell.to_s } }
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Method has too many lines. [11/10]
Open

  def tabulate(header, values, tabular = false)
    fields = []
    fields << header.map(&:to_s) unless tabular && header.all?(&:nil?)
    fields << fields.first.map { |h| h.gsub(/\S/, '-') } unless tabular
    fields += values.map { |r| r.map { |cell| cell.nil? ? '?' : cell.to_s } }
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Perceived complexity for clean_fasta_file is too high. [8/7]
Open

  def clean_fasta_file(file)
    tmp_fh = nil
    tmp_path = nil
    begin
      if file =~ /\.gz/
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Perceived complexity for tabulate is too high. [8/7]
Open

  def tabulate(header, values, tabular = false)
    fields = []
    fields << header.map(&:to_s) unless tabular && header.all?(&:nil?)
    fields << fields.first.map { |h| h.gsub(/\S/, '-') } unless tabular
    fields += values.map { |r| r.map { |cell| cell.nil? ? '?' : cell.to_s } }
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Method clean_fasta_file has 37 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def clean_fasta_file(file)
    tmp_fh = nil
    tmp_path = nil
    begin
      if file =~ /\.gz/
Severity: Minor
Found in lib/miga/common/format.rb - About 1 hr to fix

Method clean_fasta_file has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def clean_fasta_file(file)
    tmp_fh = nil
    tmp_path = nil
    begin
      if file =~ /\.gz/
Severity: Minor
Found in lib/miga/common/format.rb - About 1 hr to fix

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

Use unary plus to get an unfrozen string literal.
Open

          buffer = ''.dup
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

In Ruby 2.3 or later, use unary plus operator to unfreeze a string literal instead of String#dup and String.new. Unary plus operator is faster than String#dup.

Note: String.new (without operator) is not exactly the same as +''. These differ in encoding. String.new.encoding is always ASCII-8BIT. However, (+'').encoding is the same as script encoding(e.g. UTF-8). So, if you expect ASCII-8BIT encoding, disable this cop.

Example:

# bad
''.dup
"something".dup
String.new
String.new('')
String.new('something')

# good
+'something'
+''

Use unary plus to get an unfrozen string literal.
Open

      buffer = ''.dup
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

In Ruby 2.3 or later, use unary plus operator to unfreeze a string literal instead of String#dup and String.new. Unary plus operator is faster than String#dup.

Note: String.new (without operator) is not exactly the same as +''. These differ in encoding. String.new.encoding is always ASCII-8BIT. However, (+'').encoding is the same as script encoding(e.g. UTF-8). So, if you expect ASCII-8BIT encoding, disable this cop.

Example:

# bad
''.dup
"something".dup
String.new
String.new('')
String.new('something')

# good
+'something'
+''

Do not suppress exceptions.
Open

      rescue
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for rescue blocks with no body.

Example:

# bad

def some_method
  do_something
rescue
  # do nothing
end

Example:

# bad

begin
  do_something
rescue
  # do nothing
end

Example:

# good

def some_method
  do_something
rescue
  handle_exception
end

Example:

# good

begin
  do_something
rescue
  handle_exception
end

Avoid rescuing without specifying an error class.
Open

      rescue
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for rescuing StandardError. There are two supported styles implicit and explicit. This cop will not register an offense if any error other than StandardError is specified.

Example: EnforcedStyle: implicit

# `implicit` will enforce using `rescue` instead of
# `rescue StandardError`.

# bad
begin
  foo
rescue StandardError
  bar
end

# good
begin
  foo
rescue
  bar
end

# good
begin
  foo
rescue OtherError
  bar
end

# good
begin
  foo
rescue StandardError, SecurityError
  bar
end

Example: EnforcedStyle: explicit (default)

# `explicit` will enforce using `rescue StandardError`
# instead of `rescue`.

# bad
begin
  foo
rescue
  bar
end

# good
begin
  foo
rescue StandardError
  bar
end

# good
begin
  foo
rescue OtherError
  bar
end

# good
begin
  foo
rescue StandardError, SecurityError
  bar
end

Use && instead of and.
Open

      if (format == :fasta and ln =~ /^>/) or
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for uses of and and or, and suggests using && and || instead. It can be configured to check only in conditions, or in all contexts.

Example: EnforcedStyle: always (default)

# bad
foo.save and return

# bad
if foo and bar
end

# good
foo.save && return

# good
if foo && bar
end

Example: EnforcedStyle: conditionals

# bad
if foo and bar
end

# good
foo.save && return

# good
foo.save and return

# good
if foo && bar
end

Use && instead of and.
Open

         (format == :fastq and (i % 4) == 1)
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for uses of and and or, and suggests using && and || instead. It can be configured to check only in conditions, or in all contexts.

Example: EnforcedStyle: always (default)

# bad
foo.save and return

# bad
if foo and bar
end

# good
foo.save && return

# good
if foo && bar
end

Example: EnforcedStyle: conditionals

# bad
if foo and bar
end

# good
foo.save && return

# good
foo.save and return

# good
if foo && bar
end

Use || instead of or.
Open

      if (format == :fasta and ln =~ /^>/) or
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for uses of and and or, and suggests using && and || instead. It can be configured to check only in conditions, or in all contexts.

Example: EnforcedStyle: always (default)

# bad
foo.save and return

# bad
if foo and bar
end

# good
foo.save && return

# good
if foo && bar
end

Example: EnforcedStyle: conditionals

# bad
if foo and bar
end

# good
foo.save && return

# good
foo.save and return

# good
if foo && bar
end

Use col_n.zero? instead of col_n == 0.
Open

        col_n == 0 ? r[col_n].rjust(clen[col_n]) : r[col_n].ljust(clen[col_n])
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for usage of comparison operators (==, >, <) to test numbers as zero, positive, or negative. These can be replaced by their respective predicate methods. The cop can also be configured to do the reverse.

The cop disregards #nonzero? as it its value is truthy or falsey, but not true and false, and thus not always interchangeable with != 0.

The cop ignores comparisons to global variables, since they are often populated with objects which can be compared with integers, but are not themselves Interger polymorphic.

Example: EnforcedStyle: predicate (default)

# bad

foo == 0
0 > foo
bar.baz > 0

# good

foo.zero?
foo.negative?
bar.baz.positive?

Example: EnforcedStyle: comparison

# bad

foo.zero?
foo.negative?
bar.baz.positive?

# good

foo == 0
0 > foo
bar.baz > 0

Avoid the use of Perl-style backrefs.
Open

          id, df = $1, $2
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Redundant self detected.
Open

    o = self.dup
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for redundant uses of self.

The usage of self is only needed when:

  • Sending a message to same object with zero arguments in presence of a method name clash with an argument or a local variable.

  • Calling an attribute writer to prevent an local variable assignment.

Note, with using explicit self you can only send messages with public or protected scope, you cannot send private messages this way.

Note we allow uses of self with operators because it would be awkward otherwise.

Example:

# bad
def foo(bar)
  self.baz
end

# good
def foo(bar)
  self.bar  # Resolves name clash with the argument.
end

def foo
  bar = 1
  self.bar  # Resolves name clash with the local variable.
end

def foo
  %w[x y z].select do |bar|
    self.bar == bar  # Resolves name clash with argument of the block.
  end
end

Use || instead of or.
Open

      elsif format == :fasta or (i % 4) == 2
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for uses of and and or, and suggests using && and || instead. It can be configured to check only in conditions, or in all contexts.

Example: EnforcedStyle: always (default)

# bad
foo.save and return

# bad
if foo and bar
end

# good
foo.save && return

# good
if foo && bar
end

Example: EnforcedStyle: conditionals

# bad
if foo and bar
end

# good
foo.save && return

# good
foo.save and return

# good
if foo && bar
end

Do not use parallel assignment.
Open

          id, df = $1, $2
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

Checks for simple usages of parallel assignment. This will only complain when the number of variables being assigned matched the number of assigning variables.

Example:

# bad
a, b, c = 1, 2, 3
a, b, c = [1, 2, 3]

# good
one, two = *foo
a, b = foo()
a, b = b, a

a = 1
b = 2
c = 3

Use safe navigation (&.) instead of checking if an object exists before calling the method.
Open

        tmp_fh.close unless tmp_fh.nil?
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop transforms usages of a method call safeguarded by a non nil check for the variable whose method is being called to safe navigation (&.).

Configuration option: ConvertCodeThatCanStartToReturnNil The default for this is false. When configured to true, this will check for code in the format !foo.nil? && foo.bar. As it is written, the return of this code is limited to false and whatever the return of the method is. If this is converted to safe navigation, foo&.bar can start returning nil as well as what the method returns.

Example:

# bad
foo.bar if foo
foo.bar(param1, param2) if foo
foo.bar { |e| e.something } if foo
foo.bar(param) { |e| e.something } if foo

foo.bar if !foo.nil?
foo.bar unless !foo
foo.bar unless foo.nil?

foo && foo.bar
foo && foo.bar(param1, param2)
foo && foo.bar { |e| e.something }
foo && foo.bar(param) { |e| e.something }

# good
foo&.bar
foo&.bar(param1, param2)
foo&.bar { |e| e.something }
foo&.bar(param) { |e| e.something }

foo.nil? || foo.bar
!foo || foo.bar

# Methods that `nil` will `respond_to?` should not be converted to
# use safe navigation
foo.to_i if foo

Avoid multi-line ternary operators, use if or unless instead.
Open

      o[:med] = o[:n].even? ?
            0.5 * l[o[:n] / 2 - 1, 2].inject(:+) :
            l[(o[:n] - 1) / 2]
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for multi-line ternary op expressions.

Example:

# bad
a = cond ?
  b : c
a = cond ? b :
    c
a = cond ?
    b :
    c

# good
a = cond ? b : c
a =
  if cond
    b
  else
    c
  end

Avoid multi-line ternary operators, use if or unless instead.
Open

    clen = tabular ? Array.new(header.size, 0) :
          fields.map { |r| r.map(&:length) }.transpose.map(&:max)
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for multi-line ternary op expressions.

Example:

# bad
a = cond ?
  b : c
a = cond ? b :
    c
a = cond ?
    b :
    c

# good
a = cond ? b : c
a =
  if cond
    b
  else
    c
  end

Avoid the use of Perl-style backrefs.
Open

          id, df = $1, $2
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

There are no issues that match your filters.

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