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lib/gamtools/call_windows.py

Summary

Maintainability
B
4 hrs
Test Coverage

File call_windows.py has 299 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""
=======================
The call_windows module
=======================
Severity: Minor
Found in lib/gamtools/call_windows.py - About 3 hrs to fix

    Cyclomatic complexity is too high in function pct_orphan_windows. (6)
    Open

    def pct_orphan_windows(positive_windows):
    """Given an array of windows, calculate the percentage of orphan
    windows (positive windows not neighbouring other positive windows).

    :param positive_windows: Array representing positive or negative windows.
    Severity: Minor
    Found in lib/gamtools/call_windows.py by radon

    Cyclomatic Complexity

    Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

    Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

    Construct Effect on CC Reasoning
    if +1 An if statement is a single decision.
    elif +1 The elif statement adds another decision.
    else +0 The else statement does not cause a new decision. The decision is at the if.
    for +1 There is a decision at the start of the loop.
    while +1 There is a decision at the while statement.
    except +1 Each except branch adds a new conditional path of execution.
    finally +0 The finally block is unconditionally executed.
    with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
    assert +1 The assert statement internally roughly equals a conditional statement.
    Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
    Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

    Source: http://radon.readthedocs.org/en/latest/intro.html

    Function threshold_file has 7 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def threshold_file(input_file, output_file, #pylint: disable=too-many-arguments
    Severity: Major
    Found in lib/gamtools/call_windows.py - About 50 mins to fix

      Line too long (83 > 79 characters)
      Open

          plot_coverage_histogram(sample_name, sample_coverage_data, sample_fitting_data)
      Severity: Minor
      Found in lib/gamtools/call_windows.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.

      Indentation contains tabs
      Open

                       min_reads=None):
      Severity: Minor
      Found in lib/gamtools/call_windows.py by pep8

      On new projects, spaces-only are strongly recommended over tabs.

      Okay: if True:\n    return
W191: if True:\n\treturn

      Indentation contains mixed spaces and tabs
      Open

                       min_reads=None):
      Severity: Minor
      Found in lib/gamtools/call_windows.py by pep8

      Never mix tabs and spaces.

      The most popular way of indenting Python is with spaces only.  The
second-most popular way is with tabs only.  Code indented with a
mixture of tabs and spaces should be converted to using spaces
exclusively.  When invoking the Python command line interpreter with
the -t option, it issues warnings about code that illegally mixes
tabs and spaces.  When using -tt these warnings become errors.
These options are highly recommended!

Okay: if a == 0:\n    a = 1\n    b = 1
E101: if a == 0:\n        a = 1\n\tb = 1

      At least two spaces before inline comment
      Open

      def threshold_file(input_file, output_file, #pylint: disable=too-many-arguments
      Severity: Minor
      Found in lib/gamtools/call_windows.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 (80 > 79 characters)
      Open

          check that the value is not exactly double any of the other 20 most frequent
      Severity: Minor
      Found in lib/gamtools/call_windows.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 (88 > 79 characters)
      Open

          def fixed_threshold_fitting(sample_coverage_data): # pylint: disable=unused-argument
      Severity: Minor
      Found in lib/gamtools/call_windows.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

                  optimal_threshold = np.clip(optimal_threshold, single_read_estimate, None)
      Severity: Minor
      Found in lib/gamtools/call_windows.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

                       min_reads=None):
      Severity: Minor
      Found in lib/gamtools/call_windows.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)

      Inline comment should start with '# '
      Open

      def threshold_file(input_file, output_file, #pylint: disable=too-many-arguments
      Severity: Minor
      Found in lib/gamtools/call_windows.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 erode(coverage_data, prob):
      Severity: Minor
      Found in lib/gamtools/call_windows.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

      At least two spaces before inline comment
      Open

          def fixed_threshold_fitting(sample_coverage_data): # pylint: disable=unused-argument
      Severity: Minor
      Found in lib/gamtools/call_windows.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

      Indentation contains mixed spaces and tabs
      Open

          """
      Severity: Minor
      Found in lib/gamtools/call_windows.py by pep8

      Never mix tabs and spaces.

      The most popular way of indenting Python is with spaces only.  The
second-most popular way is with tabs only.  Code indented with a
mixture of tabs and spaces should be converted to using spaces
exclusively.  When invoking the Python command line interpreter with
the -t option, it issues warnings about code that illegally mixes
tabs and spaces.  When using -tt these warnings become errors.
These options are highly recommended!

Okay: if a == 0:\n    a = 1\n    b = 1
E101: if a == 0:\n        a = 1\n\tb = 1

      Line too long (82 > 79 characters)
      Open

          Specifically, find the most frequent non-zero entry in the coverage matrix and
      Severity: Minor
      Found in lib/gamtools/call_windows.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.

      Too many blank lines (3)
      Open

      def pct_orphan_windows(positive_windows):
      Severity: Minor
      Found in lib/gamtools/call_windows.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 (81 > 79 characters)
      Open

          entries (in case the most frequent value does not represent one read). Return
      Severity: Minor
      Found in lib/gamtools/call_windows.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

          :returns: segregation_table (a :ref:`segregation table <segregation_table>`) and \
      Severity: Minor
      Found in lib/gamtools/call_windows.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

              """ Find a coverage threshold that gives the minimum percentage of orphan
      Severity: Minor
      Found in lib/gamtools/call_windows.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 (98 > 79 characters)
      Open

      def plot_fitting_and_save(sample_name, fitting_folder, sample_coverage_data, sample_fitting_data):
      Severity: Minor
      Found in lib/gamtools/call_windows.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

          plt.axvline(np.log10(sample_fitting_data['coverage_threshold']) + (bar_width / 2),
      Severity: Minor
      Found in lib/gamtools/call_windows.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 (84 > 79 characters)
      Open

      def plot_coverage_histogram(sample_name, sample_coverage_data, sample_fitting_data):
      Severity: Minor
      Found in lib/gamtools/call_windows.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 (87 > 79 characters)
      Open

          bottom_percentile, top_percentile = (int(pct) for pct in percentile_str.split(','))
      Severity: Minor
      Found in lib/gamtools/call_windows.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.

      There are no issues that match your filters.

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