.. pylibseq documentation master file, created by
   sphinx-quickstart on Mon Oct 19 19:11:29 2015.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to pylibseq's documentation!
=================================================

If you use `pylibseq` in your research please cite the following papers: :cite:`Thornton2003-wj`

Contents:

.. toctree::
   :maxdepth: 2

   pages/changes
   pages/vmatrix
   pages/summstats
   pages/treesequences
   pages/deprecated_overview
   pages/lifetimes 
   pages/zreferences.rst

Functions and classes
##########################################

.. autoclass:: libsequence.VariantMatrix
   :members:

.. autoclass:: libsequence.AlleleCountMatrix
   :members:

.. autoclass:: libsequence.ColView
   :members:

.. autoclass:: libsequence.ConstColView
   :members:

.. autoclass:: libsequence.RowView
   :members:

.. autoclass:: libsequence.ConstRowView
   :members:

.. autoclass:: libsequence.StateCounts
   :members:

Deprecated functions and classes
##########################################


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`