.. _aldy_api:

API documentation
*****************


Major modules
=============

aldy.gene module
----------------

.. automodule:: aldy.gene
    :members:
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aldy.profile module
-------------------

.. automodule:: aldy.profile
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aldy.sam module
---------------

.. automodule:: aldy.sam
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aldy.coverage module
--------------------

.. automodule:: aldy.coverage
    :members:
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Genotyping modules
==================

aldy.genotype module
--------------------

.. automodule:: aldy.genotype
    :members:
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aldy.cn module
--------------

.. automodule:: aldy.cn
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aldy.major module
-----------------

.. automodule:: aldy.major
    :members:
    :undoc-members:
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aldy.minor module
-----------------

.. automodule:: aldy.minor
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aldy.diplotype module
---------------------

.. automodule:: aldy.diplotype
    :members:
    :undoc-members:
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Auxiliary modules
=================

aldy.common module
------------------

.. automodule:: aldy.common
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aldy.lpinterface module
-----------------------

.. automodule:: aldy.lpinterface
    :members:
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