Commit cb1ad6df authored by Steffen Möller's avatar Steffen Möller

New upstream version 0.8.1

parent 08b4a484
......@@ -5,6 +5,7 @@ os:
## - osx
python:
- 2.7
- 3.3
addons:
apt:
packages:
......
https://bitbucket.org/james_taylor/python-lzo-static/get/63987d89fd1b.zip
numpy
six
This diff is collapsed.
......@@ -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: