hapsburg.emissions_lowmem
=========================

.. py:module:: hapsburg.emissions_lowmem

.. autoapi-nested-parse::

   Class for calculating Emission Probabilities in a memory-efficient way.
   Specifically, it computes emission probability for the non-ROH state and the ROH state (only two states, 0 or 1).
   The original implementation computes the emission probability for all ROH states,
   which scales linearly with the number of haplotypes in the reference panel.
   Contains Sub-Classes, as well as a factory Method.
   @ Author: Yilei Huang, 2024, All rights reserved



Classes
-------

.. autoapisummary::

   hapsburg.emissions_lowmem.Emissions
   hapsburg.emissions_lowmem.Model_Emissions
   hapsburg.emissions_lowmem.RC_Model_Emissions
   hapsburg.emissions_lowmem.Diploid_GT_Emissions
   hapsburg.emissions_lowmem.RC_Model_Emissions_withContamination


Functions
---------

.. autoapisummary::

   hapsburg.emissions_lowmem.load_emission_model_lowmem


Module Contents
---------------

.. py:class:: Emissions(ref_haps=[], blocksize=8, overhang=0)

   Bases: :py:obj:`object`


   Class for emission probabilities
   Has methods to return emission probabilities


   .. py:attribute:: p
      :value: []



   .. py:attribute:: ref_haps
      :value: []



   .. py:attribute:: e_rate
      :value: 0.01



   .. py:attribute:: e_rate_ref
      :value: 0.001



   .. py:attribute:: overhang
      :value: 0



   .. py:attribute:: blocksize
      :value: 8



   .. py:method:: allele_freq_per_block(gts_one_block)

      Calculate allele frequency per block.
      Return 1D array of length blocksize



   .. py:method:: calc_allelefreq_blockwise()

      Calculate allele frequency for all markers in ref_haps, blockwise



   .. py:method:: give_emission(ob_stat)
      :abstractmethod:


      Gives the emission matrix of path of states
      Return emission matrix [3,l]



   .. py:method:: set_params(**kwargs)

      Set the Parameters.
      Takes keyworded arguments



.. py:class:: Model_Emissions(ref_haps=[], blocksize=8, overhang=0)

   Bases: :py:obj:`Emissions`


   Implements the haploid model Emission probabilities


   .. py:method:: give_emission(ob_stat)

      Return the full emission Probability directly in Log Space.
      ob_stat: Observed Genotypes [2,l] (only use 1st row)



.. py:class:: RC_Model_Emissions(ref_haps=[], blocksize=8, overhang=0)

   Bases: :py:obj:`Emissions`


   Implements the Read Count model Emission probabilities.


   .. py:method:: give_emission(ob_stat)

      Gives the emission matrix of path of states
      Return emission matrix [3,l]



.. py:class:: Diploid_GT_Emissions(ref_haps=[], blocksize=8, overhang=0)

   Bases: :py:obj:`Emissions`


   Implements the Diploid Genotype model Emission probabilities.


   .. py:method:: give_emission(ob_stat)

      Gives the emission matrix of path of states
      Return emission matrix [3,l]



.. py:class:: RC_Model_Emissions_withContamination(ref_haps, c, pCon, blocksize=8, overhang=0)

   Bases: :py:obj:`Emissions`


   Class for emission probabilities
   Has methods to return emission probabilities


   .. py:attribute:: c
      :value: 0.0



   .. py:attribute:: pCon
      :value: []



   .. py:method:: give_emission(ob_stat)

      Gives the emission matrix of path of states
      Return emission matrix [3,l]



.. py:function:: load_emission_model_lowmem(ref_states, e_model='haploid', c=0.0, pCon=[], overhang=0)

   Load the Emission Model