...
 
Commits (4)
......@@ -22,19 +22,3 @@ nose*.egg
# .eggs directory
.eggs
# quilt
.pc/
.pybuild/
# Debian-generated files
debian/debhelper-build-stamp
debian/files
debian/python-bx.debhelper.log
debian/python-bx.substvars
debian/python-bx/
debian/python3-bx.debhelper.log
debian/python3-bx.substvars
debian/python3-bx/
debian/tmp/
......@@ -5,6 +5,7 @@ os:
## - osx
python:
- 2.7
- 3.3
addons:
apt:
packages:
......
......@@ -3,7 +3,7 @@ python-bx for Debian
The situation is somewhat unfortunate in that both python2 and python3 occupy the same location in /usr/bin. The -tools packages separate those binaries from the modules.
The language suffix ".py" was left for the time being, uncertain about reverse dependencies.
The language suffix ".py" was left for the time being for compatibility with the installation of the same on other distributions and wary of reverse dependencies.
--
Steffen Moeller <moeller@debian.org> Sat, 14 Jan 2017 10:43:03 +0100
python-bx (0.7.4-1) unstable; urgency=low
python-bx (0.8.1-1) unstable; urgency=low
* New upstream version.
* Initial release (Closes: #851242)
* Policy compliance with 4.1.4.
-- Steffen Moeller <moeller@debian.org> Mon, 11 Jun 2018 00:33:54 +0200
python-bx (0.7.4-1) unstable; urgency=low
* Added Michael and Steffen as uploaders
* Removing generated files from source tree in debian/copyright
* Added -tools packages to separate command line interface
......
......@@ -19,10 +19,10 @@ Build-Depends:
python3-nose,
python3-numpy,
cython3
Standards-Version: 3.9.8
Standards-Version: 4.1.4
Homepage: https://github.com/bxlab/bx-python
Vcs-Git: https://anonscm.debian.org/git/debian-med/python-bx.git
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-bx.git
Vcs-Git: https://salsa.debian.org/med-team/python-bx.git
Vcs-Browser: https://salsa.debian.org/med-team/python-bx
Package: python-bx
Architecture: any
......
......@@ -7,11 +7,28 @@ Files-Excluded: lib/bx/bbi/bbi_file.h lib/bx/_seqmapping.c lib/bx/bitset.c lib/b
Files: *
Copyright: 2005-2015 The Pennsylvania State University
James Taylor <james@bx.psu.edu>
Bob Harris <rsharris@bx.psu.edu>
2013-2015 The Johns Hopkins University
License: MIT
Files: lib/bx_extras/fpconst.py
Copyright: Gregory R. Warnes <gregory_r_warnes@groton.pfizer.com
License: MIT
Files: lib/bx_extras/lrucache.py
Copyright: 2004 Evan Prodromou <evan@bad.dynu.ca>
License: AFL-2.1
Files: lib/bx_extras/pstat.py
lib/bx_extras/stats.py
Copyright: 1999-2002 Gary Strangman
License: GPL-2
Files: debian/*
Copyright: 2016 Afif Elghraoui <afif@debian.org>
Copyright: 2016 Afif Elghraoui <afif@debian.org>
2017-8 Steffen Moeller <moeller@debian.org>
License: MIT
License: MIT
......@@ -32,3 +49,182 @@ License: MIT
CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
License: GPL-2.0
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>
.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
License: AFL-2.1
The Academic Free License
v.2.1
.
This Academic Free License (the "License") applies to any original
work of authorship (the "Original Work") whose owner (the "Licensor")
has placed the following notice immediately following the copyright
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Licensed under the Academic Free License version 2.1
1) Grant of Copyright License. Licensor hereby grants You a
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relating thereto, the prevailing party shall be entitled to recover
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13)Miscellaneous.
This License represents the complete agreement concerning the
subject matter hereof. If any provision of this License is held
to be unenforceable, such provision shall be reformed only to the
extent necessary to make it enforceable.
14) Definition of "You" in This License.
"You" throughout this License, whether in upper or lower case,
means an individual or a legal entity exercising rights under, and
complying with all of the terms of, this License. For legal entities,
"You" includes any entity that controls, is controlled by, or is under
common control with you. For purposes of this definition, "control"
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15) Right to Use.
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reserved. Permission is hereby granted to copy and distribute this
license without modification. This license may not be modified without
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Standard License Header
.
Licensed under the Academic Free License version 2.1
......@@ -6,7 +6,7 @@ Index: python-bx/setup.py
===================================================================
--- python-bx.orig/setup.py
+++ python-bx/setup.py
@@ -7,8 +7,8 @@ if sys.version_info < (2, 4):
@@ -9,8 +9,8 @@ elif sys.version_info > (3, ) and sys.ve
try:
from setuptools import setup, find_packages
except ImportError:
......
https://bitbucket.org/james_taylor/python-lzo-static/get/63987d89fd1b.zip
numpy
six
# -*- coding: utf-8 -*-
#
# BxPython documentation build configuration file, created by
# sphinx-quickstart on Fri May 08 10:18:22 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# The contents of this file are pickled, so don't put values in the namespace
# that aren't pickleable (module imports are okay, they're removed automatically).
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys, os
# If your extensions are in another directory, add it here. If the directory
# is relative to the documentation root, use os.path.abspath to make it
# absolute, like shown here.
#sys.path.append(os.path.abspath('.'))
curr_dir = os.path.dirname( __file__ )
bx_dir = os.path.join( curr_dir, '..', '..', 'lib')
sys.path.insert( 0, bx_dir )
import bx
# General configuration
# ---------------------
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'bx-python'
copyright = u'2009, James Taylor'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = bx.__version__
# The full version, including alpha/beta/rc tags.
release = version
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of documents that shouldn't be included in the build.
#unused_docs = []
# List of directories, relative to source directory, that shouldn't be searched
# for source files.
exclude_trees = []
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# Options for HTML output
# -----------------------
# The style sheet to use for HTML and HTML Help pages. A file of that name
# must exist either in Sphinx' static/ path, or in one of the custom paths
# given in html_static_path.
html_style = 'base.css'
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['static']
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
html_index = 'index.html'
html_sidebars = { 'index': 'indexsidebar.html'}
# Additional templates that should be rendered to pages, maps page names to
# template names.
##html_additional_pages = {
## 'index': 'index.html',
##}
# If false, no module index is generated.
#html_use_modindex = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, the reST sources are included in the HTML build as _sources/<name>.
#html_copy_source = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = ''
# Output file base name for HTML help builder.
htmlhelp_basename = 'bx-doc'
# Options for LaTeX output
# ------------------------
# The paper size ('letter' or 'a4').
#latex_paper_size = 'letter'
# The font size ('10pt', '11pt' or '12pt').
#latex_font_size = '10pt'
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, document class [howto/manual]).
latex_documents = [
('index', 'bx-python.tex', ur'bx-python Documentation',
ur'James Taylor', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# Additional stuff for the LaTeX preamble.
#latex_preamble = ''
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_use_modindex = True
# Example configuration for intersphinx: refer to the Python standard library.
#intersphinx_mapping = {'http://docs.python.org/dev': None}
# -*- coding: utf-8 -*-
#
# BxPython documentation build configuration file, created by
# sphinx-quickstart on Fri May 08 10:18:22 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# The contents of this file are pickled, so don't put values in the namespace
# that aren't pickleable (module imports are okay, they're removed automatically).
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys, os
# If your extensions are in another directory, add it here. If the directory
# is relative to the documentation root, use os.path.abspath to make it
# absolute, like shown here.
#sys.path.append(os.path.abspath('.'))
## curr_dir = os.path.dirname( __file__ )
## bx_dir = os.path.join( curr_dir, '..', '..', 'lib')
## sys.path.insert( 0, bx_dir )
import bx
# General configuration
# ---------------------
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'bx-python'
copyright = u'2017, James Taylor'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = bx.__version__
# The full version, including alpha/beta/rc tags.
release = version
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of documents that shouldn't be included in the build.
#unused_docs = []
# List of directories, relative to source directory, that shouldn't be searched
# for source files.
exclude_trees = []
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# Options for HTML output
# -----------------------
# The style sheet to use for HTML and HTML Help pages. A file of that name
# must exist either in Sphinx' static/ path, or in one of the custom paths
# given in html_static_path.
html_style = 'base.css'
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['static']
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
html_index = 'index.html'
html_sidebars = { 'index': 'indexsidebar.html'}
# Additional templates that should be rendered to pages, maps page names to
# template names.
##html_additional_pages = {
## 'index': 'index.html',
##}
# If false, no module index is generated.
#html_use_modindex = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, the reST sources are included in the HTML build as _sources/<name>.
#html_copy_source = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = ''
# Output file base name for HTML help builder.
htmlhelp_basename = 'bx-doc'
# Options for LaTeX output
# ------------------------
# The paper size ('letter' or 'a4').
#latex_paper_size = 'letter'
# The font size ('10pt', '11pt' or '12pt').
#latex_font_size = '10pt'
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, document class [howto/manual]).
latex_documents = [
('index', 'bx-python.tex', ur'bx-python Documentation',
ur'James Taylor', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# Additional stuff for the LaTeX preamble.
#latex_preamble = ''
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_use_modindex = True
# Example configuration for intersphinx: refer to the Python standard library.
#intersphinx_mapping = {'http://docs.python.org/dev': None}
......@@ -15,9 +15,9 @@ Contents
========
.. toctree::
:maxdepth: 2
:maxdepth: 5
modules/index.rst
Application Documentation <lib/modules>
Indices and tables
==================
......
bx.align.axt module
===================
.. automodule:: bx.align.axt
:members:
:undoc-members:
:show-inheritance:
bx.align.core module
====================
.. automodule:: bx.align.core
:members:
:undoc-members:
:show-inheritance:
bx.align.epo module
===================
.. automodule:: bx.align.epo
:members:
:undoc-members:
:show-inheritance:
bx.align.epo_tests module
=========================
.. automodule:: bx.align.epo_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.lav module
===================
.. automodule:: bx.align.lav
:members:
:undoc-members:
:show-inheritance:
bx.align.lav_tests module
=========================
.. automodule:: bx.align.lav_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.maf module
===================
.. automodule:: bx.align.maf
:members:
:undoc-members:
:show-inheritance:
bx.align.maf_tests module
=========================
.. automodule:: bx.align.maf_tests
:members:
:undoc-members:
:show-inheritance:
bx.align package
================
Subpackages
-----------
.. toctree::
bx.align.sitemask
bx.align.tools
Submodules
----------
.. toctree::
bx.align.axt
bx.align.core
bx.align.epo
bx.align.epo_tests
bx.align.lav
bx.align.lav_tests
bx.align.maf
bx.align.maf_tests
bx.align.score
bx.align.score_tests
Module contents
---------------
.. automodule:: bx.align
:members:
:undoc-members:
:show-inheritance:
bx.align.score module
=====================
.. automodule:: bx.align.score
:members:
:undoc-members:
:show-inheritance:
bx.align.score_tests module
===========================
.. automodule:: bx.align.score_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.core module
=============================
.. automodule:: bx.align.sitemask.core
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.cpg module
============================
.. automodule:: bx.align.sitemask.cpg
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.quality module
================================
.. automodule:: bx.align.sitemask.quality
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask package
=========================
Submodules
----------
.. toctree::
bx.align.sitemask.core
bx.align.sitemask.cpg
bx.align.sitemask.quality
bx.align.sitemask.sitemask_tests
Module contents
---------------
.. automodule:: bx.align.sitemask
:members:
:undoc-members:
:show-inheritance:
bx.align.sitemask.sitemask_tests module
=======================================
.. automodule:: bx.align.sitemask.sitemask_tests
:members:
:undoc-members:
:show-inheritance:
bx.align.tools.chop module
==========================
.. automodule:: bx.align.tools.chop
:members:
:undoc-members:
:show-inheritance:
bx.align.tools.fuse module
==========================
.. automodule:: bx.align.tools.fuse
:members:
:undoc-members:
:show-inheritance:
bx.align.tools package
======================
Submodules
----------
.. toctree::
bx.align.tools.chop
bx.align.tools.fuse
bx.align.tools.thread
bx.align.tools.tile
Module contents
---------------
.. automodule:: bx.align.tools
:members:
:undoc-members:
:show-inheritance:
bx.align.tools.thread module
============================
.. automodule:: bx.align.tools.thread
:members:
:undoc-members:
:show-inheritance:
bx.align.tools.tile module
==========================
.. automodule:: bx.align.tools.tile
:members:
:undoc-members:
:show-inheritance:
bx.arrays.array_tree module
===========================
.. automodule:: bx.arrays.array_tree
:members:
:undoc-members:
:show-inheritance:
bx.arrays.array_tree_tests module
=================================
.. automodule:: bx.arrays.array_tree_tests
:members:
:undoc-members:
:show-inheritance:
bx.arrays.bed module
====================
.. automodule:: bx.arrays.bed
:members:
:undoc-members:
:show-inheritance:
bx.arrays package
=================
Submodules
----------
.. toctree::
bx.arrays.array_tree
bx.arrays.array_tree_tests
bx.arrays.bed
bx.arrays.wiggle
Module contents
---------------
.. automodule:: bx.arrays
:members:
:undoc-members:
:show-inheritance:
bx.arrays.wiggle module
=======================
.. automodule:: bx.arrays.wiggle
:members:
:undoc-members:
:show-inheritance:
bx.bbi.bbi_file module
======================
.. automodule:: bx.bbi.bbi_file
:members:
:undoc-members:
:show-inheritance:
bx.bbi.bigbed_file module
=========================
.. automodule:: bx.bbi.bigbed_file
:members:
:undoc-members:
:show-inheritance:
bx.bbi.bigwig_file module
=========================
.. automodule:: bx.bbi.bigwig_file
:members:
:undoc-members:
:show-inheritance:
bx.bbi.bigwig_tests module
==========================
.. automodule:: bx.bbi.bigwig_tests
:members:
:undoc-members:
:show-inheritance:
bx.bbi.bpt_file module
======================
.. automodule:: bx.bbi.bpt_file
:members:
:undoc-members:
:show-inheritance:
bx.bbi.cirtree_file module
==========================
.. automodule:: bx.bbi.cirtree_file
:members:
:undoc-members:
:show-inheritance:
bx.bbi package
==============
Submodules
----------
.. toctree::
bx.bbi.bbi_file
bx.bbi.bigbed_file
bx.bbi.bigwig_file
bx.bbi.bigwig_tests
bx.bbi.bpt_file
bx.bbi.cirtree_file
Module contents
---------------
.. automodule:: bx.bbi
:members:
:undoc-members:
:show-inheritance:
bx.binned_array module
======================
.. automodule:: bx.binned_array
:members:
:undoc-members:
:show-inheritance:
bx.binned_array_tests module
============================
.. automodule:: bx.binned_array_tests
:members:
:undoc-members:
:show-inheritance:
bx.bitset module
================
.. automodule:: bx.bitset
:members:
:undoc-members:
:show-inheritance:
bx.bitset_builders module
=========================
.. automodule:: bx.bitset_builders
:members:
:undoc-members:
:show-inheritance:
bx.bitset_tests module
======================
.. automodule:: bx.bitset_tests
:members:
:undoc-members:
:show-inheritance:
bx.bitset_utils module
======================
.. automodule:: bx.bitset_utils
:members:
:undoc-members:
:show-inheritance:
bx.cookbook.argparse module
===========================
.. automodule:: bx.cookbook.argparse
:members:
:undoc-members:
:show-inheritance:
bx.cookbook.attribute module
============================
.. automodule:: bx.cookbook.attribute
:members:
:undoc-members:
:show-inheritance:
bx.cookbook.doc_optparse module
===============================
.. automodule:: bx.cookbook.doc_optparse
:members:
:undoc-members:
:show-inheritance:
bx.cookbook.progress_bar module
===============================
.. automodule:: bx.cookbook.progress_bar
:members:
:undoc-members:
:show-inheritance:
bx.cookbook package
===================
Submodules
----------
.. toctree::
bx.cookbook.argparse
bx.cookbook.attribute
bx.cookbook.doc_optparse
bx.cookbook.progress_bar
Module contents
---------------
.. automodule:: bx.cookbook
:members:
:undoc-members:
:show-inheritance:
bx.filter module
================
.. automodule:: bx.filter
:members:
:undoc-members:
:show-inheritance:
bx.gene_reader module
=====================
.. automodule:: bx.gene_reader
:members:
:undoc-members:
:show-inheritance:
bx.interval_index_file module
=============================
.. automodule:: bx.interval_index_file
:members:
:undoc-members:
:show-inheritance:
bx.interval_index_file_tests module
===================================
.. automodule:: bx.interval_index_file_tests
:members:
:undoc-members:
:show-inheritance:
bx.intervals.cluster module
===========================
.. automodule:: bx.intervals.cluster
:members:
:undoc-members:
:show-inheritance:
bx.intervals.cluster_tests module
=================================
.. automodule:: bx.intervals.cluster_tests
:members:
:undoc-members:
:show-inheritance:
bx.intervals.intersection module
================================
.. automodule:: bx.intervals.intersection
:members:
:undoc-members:
:show-inheritance:
bx.intervals.intersection_tests module
======================================
.. automodule:: bx.intervals.intersection_tests
:members:
:undoc-members:
:show-inheritance:
bx.intervals.io module
======================
.. automodule:: bx.intervals.io
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.base_coverage module
============================================
.. automodule:: bx.intervals.operations.base_coverage
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.complement module
=========================================
.. automodule:: bx.intervals.operations.complement
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.concat module
=====================================
.. automodule:: bx.intervals.operations.concat
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.coverage module
=======================================
.. automodule:: bx.intervals.operations.coverage
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.find_clusters module
============================================
.. automodule:: bx.intervals.operations.find_clusters
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.intersect module
========================================
.. automodule:: bx.intervals.operations.intersect
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.join module
===================================
.. automodule:: bx.intervals.operations.join
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.merge module
====================================
.. automodule:: bx.intervals.operations.merge
:members:
:undoc-members:
:show-inheritance:
bx.intervals.operations.quicksect module
========================================
.. automodule:: bx.intervals.operations.quicksect
:members:
:undoc-members:
:show-inheritance: