pombo-lab/gamtools

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lib/gamtools/resolution.py

Summary

Maintainability
B
4 hrs
Test Coverage

Function do_segregation_qc has 9 arguments (exceeds 4 allowed). Consider refactoring.
Open

def do_segregation_qc(segregation_table, slice_thickness, nuclear_radius, coverage_q=0.2, #pylint: disable=too-many-arguments
Severity: Major
Found in lib/gamtools/resolution.py - About 1 hr to fix

    Function get_detection_efficiency has 8 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def get_detection_efficiency(segregation_table, slice_thickness, #pylint: disable=too-many-arguments
    Severity: Major
    Found in lib/gamtools/resolution.py - About 1 hr to fix

      Function do_segregation_qc has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
      Open

      def do_segregation_qc(segregation_table, slice_thickness, nuclear_radius, coverage_q=0.2, #pylint: disable=too-many-arguments
                            skip_chroms=None, genome_size=None, plexity=1, only_visible=True):
          """
          Check that a GAM dataset has sufficient quality and depth.  Specifically,
          check that 80% of genomic windows have been detected at least 20 times
      Severity: Minor
      Found in lib/gamtools/resolution.py - About 45 mins 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

      Identical blocks of code found in 2 locations. Consider refactoring.
      Open

          if only_visible:
              visible = segregation_table.loc[segregation_table.sum(axis=1) > 0]
          else:
              visible = segregation_table
      Severity: Minor
      Found in lib/gamtools/resolution.py and 1 other location - About 55 mins to fix
      lib/gamtools/resolution.py on lines 158..161

      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 37.

      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

      Further Reading

      Identical blocks of code found in 2 locations. Consider refactoring.
      Open

          if only_visible:
              visible = segregation_table.loc[segregation_table.sum(axis=1) > 0]
          else:
              visible = segregation_table
      Severity: Minor
      Found in lib/gamtools/resolution.py and 1 other location - About 55 mins to fix
      lib/gamtools/resolution.py on lines 118..121

      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 37.

      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

      Further Reading

      Line too long (80 > 79 characters)
      Open

      in the dataset with a sufficient frequency. We recommend that 80% of the windows
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (83 > 79 characters)
      Open

          :param float window_fraction: Genomic window size divided by total genome size.
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (80 > 79 characters)
      Open

                                   nuclear_radius, skip_chroms=None, genome_size=None,
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (80 > 79 characters)
      Open

          :param float quantile: The quantile at which to calculate window coverage. \
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (81 > 79 characters)
      Open

                never detected across the dataset in calculation. This is the default \
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (83 > 79 characters)
      Open

          :returns: Number of libraries, total size of the genome and size of each window
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (85 > 79 characters)
      Open

          segregation_windows = segregation_table.reset_index()[['chrom', 'start', 'stop']]
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (82 > 79 characters)
      Open

          :param float coverage_q: The quantile at which to calculate window coverage. \
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Expected 2 blank lines, found 1
      Open

      def resolution_check_from_args(args):
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Separate top-level function and class definitions with two blank lines.

      Method definitions inside a class are separated by a single blank
      line.
      
      Extra blank lines may be used (sparingly) to separate groups of
      related functions.  Blank lines may be omitted between a bunch of
      related one-liners (e.g. a set of dummy implementations).
      
      Use blank lines in functions, sparingly, to indicate logical
      sections.
      
      Okay: def a():\n    pass\n\n\ndef b():\n    pass
      Okay: def a():\n    pass\n\n\nasync def b():\n    pass
      Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
      Okay: default = 1\nfoo = 1
      Okay: classify = 1\nfoo = 1
      
      E301: class Foo:\n    b = 0\n    def bar():\n        pass
      E302: def a():\n    pass\n\ndef b(n):\n    pass
      E302: def a():\n    pass\n\nasync def b(n):\n    pass
      E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
      E303: def a():\n\n\n\n    pass
      E304: @decorator\n\ndef a():\n    pass
      E305: def a():\n    pass\na()
      E306: def a():\n    def b():\n        pass\n    def c():\n        pass

      Line too long (86 > 79 characters)
      Open

          segregation_windows['size'] = segregation_windows.stop - segregation_windows.start
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Multiple spaces after operator
      Open

          avg_m1s_m =  visible.sum(axis=1).mean() / visible.shape[1]
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Avoid extraneous whitespace around an operator.

      Okay: a = 12 + 3
      E221: a = 4  + 5
      E222: a = 4 +  5
      E223: a = 4\t+ 5
      E224: a = 4 +\t5

      Line too long (88 > 79 characters)
      Open

                            skip_chroms=None, genome_size=None, plexity=1, only_visible=True):
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      At least two spaces before inline comment
      Open

      def do_segregation_qc(segregation_table, slice_thickness, nuclear_radius, coverage_q=0.2, #pylint: disable=too-many-arguments
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Separate inline comments by at least two spaces.

      An inline comment is a comment on the same line as a statement.
      Inline comments should be separated by at least two spaces from the
      statement. They should start with a # and a single space.
      
      Each line of a block comment starts with a # and a single space
      (unless it is indented text inside the comment).
      
      Okay: x = x + 1  # Increment x
      Okay: x = x + 1    # Increment x
      Okay: # Block comment
      E261: x = x + 1 # Increment x
      E262: x = x + 1  #Increment x
      E262: x = x + 1  #  Increment x
      E265: #Block comment
      E266: ### Block comment

      Expected 2 blank lines, found 1
      Open

      def segregation_info(segregation_table, skip_chroms):
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Separate top-level function and class definitions with two blank lines.

      Method definitions inside a class are separated by a single blank
      line.
      
      Extra blank lines may be used (sparingly) to separate groups of
      related functions.  Blank lines may be omitted between a bunch of
      related one-liners (e.g. a set of dummy implementations).
      
      Use blank lines in functions, sparingly, to indicate logical
      sections.
      
      Okay: def a():\n    pass\n\n\ndef b():\n    pass
      Okay: def a():\n    pass\n\n\nasync def b():\n    pass
      Okay: def a():\n    pass\n\n\n# Foo\n# Bar\n\ndef b():\n    pass
      Okay: default = 1\nfoo = 1
      Okay: classify = 1\nfoo = 1
      
      E301: class Foo:\n    b = 0\n    def bar():\n        pass
      E302: def a():\n    pass\n\ndef b(n):\n    pass
      E302: def a():\n    pass\n\nasync def b(n):\n    pass
      E303: def a():\n    pass\n\n\n\ndef b(n):\n    pass
      E303: def a():\n\n\n\n    pass
      E304: @decorator\n\ndef a():\n    pass
      E305: def a():\n    pass\na()
      E306: def a():\n    def b():\n        pass\n    def c():\n        pass

      Line too long (100 > 79 characters)
      Open

      def get_detection_efficiency(segregation_table, slice_thickness, #pylint: disable=too-many-arguments
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (81 > 79 characters)
      Open

                never detected across the dataset in calculation. This is the default \
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (86 > 79 characters)
      Open

                            skip_chroms=args.skip_chromosomes, genome_size=args.genome_size,
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (85 > 79 characters)
      Open

          the window size. This is important because a genomic window does not have to fall
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (86 > 79 characters)
      Open

          can fall outside of the physical section and still be 'effectively' within the NP.
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      At least two spaces before inline comment
      Open

      def get_detection_efficiency(segregation_table, slice_thickness, #pylint: disable=too-many-arguments
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Separate inline comments by at least two spaces.

      An inline comment is a comment on the same line as a statement.
      Inline comments should be separated by at least two spaces from the
      statement. They should start with a # and a single space.
      
      Each line of a block comment starts with a # and a single space
      (unless it is indented text inside the comment).
      
      Okay: x = x + 1  # Increment x
      Okay: x = x + 1    # Increment x
      Okay: # Block comment
      E261: x = x + 1 # Increment x
      E262: x = x + 1  #Increment x
      E262: x = x + 1  #  Increment x
      E265: #Block comment
      E266: ### Block comment

      Inline comment should start with '# '
      Open

      def get_detection_efficiency(segregation_table, slice_thickness, #pylint: disable=too-many-arguments
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Separate inline comments by at least two spaces.

      An inline comment is a comment on the same line as a statement.
      Inline comments should be separated by at least two spaces from the
      statement. They should start with a # and a single space.
      
      Each line of a block comment starts with a # and a single space
      (unless it is indented text inside the comment).
      
      Okay: x = x + 1  # Increment x
      Okay: x = x + 1    # Increment x
      Okay: # Block comment
      E261: x = x + 1 # Increment x
      E262: x = x + 1  #Increment x
      E262: x = x + 1  #  Increment x
      E265: #Block comment
      E266: ### Block comment

      Line too long (82 > 79 characters)
      Open

                    'the genomic window size for this dataset.'.format(window_coverage))
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (83 > 79 characters)
      Open

          do_segregation_qc(segregation_table, args.slice_thickness, args.nuclear_radius,
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (85 > 79 characters)
      Open

          table_genome_size, window_size = segregation_info(segregation_table, skip_chroms)
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (80 > 79 characters)
      Open

          :param segregation_table: Input :ref:`segregation table <segregation_table>`
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (125 > 79 characters)
      Open

      def do_segregation_qc(segregation_table, slice_thickness, nuclear_radius, coverage_q=0.2, #pylint: disable=too-many-arguments
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (80 > 79 characters)
      Open

          :param segregation_table: Input :ref:`segregation table <segregation_table>`
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (81 > 79 characters)
      Open

          :param float genome_size: Total size of the genome (if None, calculate from \
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (85 > 79 characters)
      Open

                    'least {:.0f} times. This value should be at least 20, try increasing '
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (85 > 79 characters)
      Open

          Compute the ratio between slice thickness and nuclear radius, taking into account
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (86 > 79 characters)
      Open

          entirely within the NP to be detected. The larger the window size, the further DNA
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (81 > 79 characters)
      Open

          window_coverage = get_segregation_coverage_qc(segregation_table, skip_chroms,
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Continuation line under-indented for visual indent
      Open

                                      only_visible, coverage_q)
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
      using Python's implicit line joining inside parentheses, brackets
      and braces, or using a hanging indent.
      
      When using a hanging indent these considerations should be applied:
      - there should be no arguments on the first line, and
      - further indentation should be used to clearly distinguish itself
        as a continuation line.
      
      Okay: a = (\n)
      E123: a = (\n    )
      
      Okay: a = (\n    42)
      E121: a = (\n   42)
      E122: a = (\n42)
      E123: a = (\n    42\n    )
      E124: a = (24,\n     42\n)
      E125: if (\n    b):\n    pass
      E126: a = (\n        42)
      E127: a = (24,\n      42)
      E128: a = (24,\n    42)
      E129: if (a or\n    b):\n    pass
      E131: a = (\n    42\n 24)

      Line too long (83 > 79 characters)
      Open

          :returns: Number of libraries, total size of the genome and size of each window
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (81 > 79 characters)
      Open

                never detected across the dataset in calculation. This is the default \
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Inline comment should start with '# '
      Open

      def do_segregation_qc(segregation_table, slice_thickness, nuclear_radius, coverage_q=0.2, #pylint: disable=too-many-arguments
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Separate inline comments by at least two spaces.

      An inline comment is a comment on the same line as a statement.
      Inline comments should be separated by at least two spaces from the
      statement. They should start with a # and a single space.
      
      Each line of a block comment starts with a # and a single space
      (unless it is indented text inside the comment).
      
      Okay: x = x + 1  # Increment x
      Okay: x = x + 1    # Increment x
      Okay: # Block comment
      E261: x = x + 1 # Increment x
      E262: x = x + 1  #Increment x
      E262: x = x + 1  #  Increment x
      E265: #Block comment
      E266: ### Block comment

      Line too long (81 > 79 characters)
      Open

          :param float genome_size: Total size of the genome (if None, calculate from \
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (81 > 79 characters)
      Open

      def compute_eff_slice_fraction(slice_thickness, nuclear_radius, window_fraction):
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Line too long (80 > 79 characters)
      Open

          :param segregation_table: Input :ref:`segregation table <segregation_table>`
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

      Continuation line under-indented for visual indent
      Open

                  (((1 - avg_m1s_m) ** coef) ** (1/2)))
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Continuation lines indentation.

      Continuation lines should align wrapped elements either vertically
      using Python's implicit line joining inside parentheses, brackets
      and braces, or using a hanging indent.
      
      When using a hanging indent these considerations should be applied:
      - there should be no arguments on the first line, and
      - further indentation should be used to clearly distinguish itself
        as a continuation line.
      
      Okay: a = (\n)
      E123: a = (\n    )
      
      Okay: a = (\n    42)
      E121: a = (\n   42)
      E122: a = (\n42)
      E123: a = (\n    42\n    )
      E124: a = (24,\n     42\n)
      E125: if (\n    b):\n    pass
      E126: a = (\n        42)
      E127: a = (24,\n      42)
      E128: a = (24,\n    42)
      E129: if (a or\n    b):\n    pass
      E131: a = (\n    42\n 24)

      Line too long (80 > 79 characters)
      Open

          :param segregation_table: Input :ref:`segregation table <segregation_table>`
      Severity: Minor
      Found in lib/gamtools/resolution.py by pep8

      Limit all lines to a maximum of 79 characters.

      There are still many devices around that are limited to 80 character
      lines; plus, limiting windows to 80 characters makes it possible to
      have several windows side-by-side.  The default wrapping on such
      devices looks ugly.  Therefore, please limit all lines to a maximum
      of 79 characters. For flowing long blocks of text (docstrings or
      comments), limiting the length to 72 characters is recommended.
      
      Reports error E501.

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