karyohmm API Reference
======================

This page documents the public API of the ``karyohmm`` package.

Core HMM Models
---------------

.. autoclass:: karyohmm.karyohmm.MetaHMM
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.. autoclass:: karyohmm.karyohmm.QuadHMM
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.. autoclass:: karyohmm.karyohmm.PocHMM
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   :show-inheritance:

Mosaic and Contamination Estimators
-------------------------------------

.. autoclass:: karyohmm.karyohmm.MosaicEst
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   :show-inheritance:

.. autoclass:: karyohmm.karyohmm.MccEst
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   :show-inheritance:

Recombination and Phase Correction
-------------------------------------

.. autoclass:: karyohmm.karyohmm.RecombEst
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.. autoclass:: karyohmm.karyohmm.PhaseCorrect
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   :show-inheritance:

Base Class
----------

.. autoclass:: karyohmm.karyohmm.AneuploidyHMM
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Simulators
----------

.. autoclass:: karyohmm.simulator.PGTSim
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.. autoclass:: karyohmm.simulator.PGTSimMosaic
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.. autoclass:: karyohmm.simulator.PGTSimSegmental
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.. autoclass:: karyohmm.simulator.PGTSimVCF
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.. autoclass:: karyohmm.simulator.PGTSimBase
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I/O Utilities
-------------

.. automodule:: karyohmm.io
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