Code documentation
==================

Common
---------------

.. automodule:: amplimap.common
   :members:

File reader
---------------

.. automodule:: amplimap.reader
   :members:

Read parser
---------------

.. automodule:: amplimap.parse_reads
   :members:

Alignment stats
---------------

.. automodule:: amplimap.stats_alignment
   :members:

Coverage
---------------

.. automodule:: amplimap.coverage
   :members:

Variants
---------------

.. automodule:: amplimap.variants
   :members:

Pileup
---------------

.. automodule:: amplimap.pileup
   :members:

Others
---------------

.. automodule:: amplimap.merge_folders
   :members:

.. automodule:: amplimap.naive_mapper
   :members:

.. automodule:: amplimap.run
   :members:

.. automodule:: amplimap.simulate
   :members: