.. LORALS documentation master file, created by
   sphinx-quickstart on Tue Sep 22 10:43:10 2020.
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Long Read Allele Specific analysis
==================================

LORALS is a package and collection of tools for conducting allele-specific analyses
in Oxford Nanopore-generated long read data

.. toctree::
   :maxdepth: 1
   :caption: Contents:

   cmds/index.rst


Installation
------------

LORALS is available on GitHub at https://github.com/mojaveazure/lorals and can be installed with pip

::

    pip install git+https://github.com/mojaveazure/lorals.git


.. Command-line tools
.. ------------------

.. LORALS provides the following command-line tools

.. - :code:`calc_asts`: Calculate allele specific transcript structure (asts) and allele-specific expression (ase)
.. - :code:`annotate_ase`: Annotate an ase matrix with gene IDs, genotype information, and blacklist and other warnings

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

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