Documentation
=============

Command line interface
----------------------

.. click:: happler.__main__:main
   :prog: happler
   :nested: full


Module contents
---------------

happler.tree.tree module
~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: happler.tree.tree
   :members:
   :undoc-members:
   :show-inheritance:

happler.tree.tree_builder module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: happler.tree.tree_builder
   :members:
   :undoc-members:
   :show-inheritance:

happler.tree.variant module
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: happler.tree.variant
   :members:
   :undoc-members:
   :show-inheritance:

happler.tree.haplotypes module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: happler.tree.haplotypes
   :members:
   :undoc-members:
   :show-inheritance:

happler.tree.assoc_test module
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. automodule:: happler.tree.assoc_test
   :members:
   :undoc-members:
   :show-inheritance: