API reference
=============

The public API is re-exported from the top-level :mod:`vdjmatch` package —
:class:`vdjmatch.api.Annotator` and the module-level :func:`vdjmatch.annotate` shortcut. The
submodules below expose the building blocks (VDJdb access, the search index, E-values, I/O).

vdjmatch.api
------------

.. automodule:: vdjmatch.api
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vdjmatch.db
-----------

.. automodule:: vdjmatch.db
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vdjmatch.match
--------------

.. automodule:: vdjmatch.match
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vdjmatch.evalue
---------------

.. automodule:: vdjmatch.evalue
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vdjmatch.aggregate
------------------

.. automodule:: vdjmatch.aggregate
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vdjmatch.io
-----------

.. automodule:: vdjmatch.io
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vdjmatch.cluster
----------------

.. automodule:: vdjmatch.cluster
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vdjmatch.precursor
------------------

.. note::

   Needs the optional extra: ``pip install 'vdjmatch[precursor]'``. It pulls ``vdjtools`` for the
   recombination model; importing ``vdjmatch`` itself never does.

.. automodule:: vdjmatch.precursor
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