CNVfinder's code documentation
------------------------------

.. toctree::
   :maxdepth: 2

cnvdetector
===========
.. automodule:: cnvfinder.cnvdetector
.. autoclass:: CNVTest
    :members:
.. autoclass:: CNVConfig
    :members:

nrrhandler
==========
.. automodule:: cnvfinder.nrrhandler
.. autoclass:: NRR
    :members:
.. autoclass:: NRRList
    :members:
.. autoclass:: NRRTest
    :members:
.. autoclass:: NRRConfig
    :members:
.. automethod:: cnvfinder.nrrhandler.readcount

vcfhandler
==========
.. automodule:: cnvfinder.vcfhandler
.. autoclass:: VCF
    :members:
.. autoclass:: VCFList
    :members:
.. autoclass:: VCFTest
    :members:
.. autoclass:: VCFConfig
    :members:

bedloader
=========
.. automodule:: cnvfinder.bedloader
.. autoclass:: ROI
    :members:

tsvparser
=========
.. automodule:: cnvfinder.tsvparser
.. autoclass:: CoverageFileParser
    :members:

ideogram
========
.. automodule:: cnvfinder.ideogram
.. autoclass:: Ideogram
    :members: