hapsburg.emissions
==================

.. py:module:: hapsburg.emissions

.. autoapi-nested-parse::

   Class for calculating Emission Probabilities.
   Contains Sub-Classes, as well as factory Method.
   @ Author: Harald Ringbauer, 2019, All rights reserved



Attributes
----------

.. autoapisummary::

   hapsburg.emissions.DTYPE
   hapsburg.emissions.ob_stat


Classes
-------

.. autoapisummary::

   hapsburg.emissions.Emissions
   hapsburg.emissions.Model_Emissions
   hapsburg.emissions.RC_Model_Emissions
   hapsburg.emissions.Diploid_GT_Emissions
   hapsburg.emissions.RC_Model_Emissions_withContamination


Functions
---------

.. autoapisummary::

   hapsburg.emissions.load_emission_model


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

.. py:data:: DTYPE

.. py:class:: Emissions

   Bases: :py:obj:`object`


   Class for emission probabilities
   Has methods to return emission probabilities


   .. py:method:: give_emission_matrix(remember=False)
      :abstractmethod:


      Return Emission Matrix



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


      Gives the emission matrix of path of states



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

      Set the Parameters.
      Takes keyworded arguments



.. py:class:: Model_Emissions(ref_haps=[])

   Bases: :py:obj:`Emissions`


   Implements the haploid model Emission probabilities


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



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



   .. py:attribute:: e_mat
      :value: []



   .. py:attribute:: e_rate
      :value: 0.001



   .. py:method:: give_emission_matrix(remember=False)

      Return full Emission Matrix.
      dtype: Precision of the returned Matrix



   .. py:method:: give_emission_state(ob_stat, e_mat)

      Gives the emission matrix of observed states
      Return emission matrix [k,l]



   .. 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=[])

   Bases: :py:obj:`Model_Emissions`


   Implements the Read Count model Emission probabilities.
   Inherits from Model_Emission, in particular the constructor (Calculation
   of Mean Allele Frequency from the Reference and ref_haps)


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



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



   .. py:attribute:: e_mat
      :value: []



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



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



   .. py:method:: give_emission_matrix(remember=False)

      Return Emission Matrix, which describes
      probabilities in Genotypes [n_ref+1, n_loci, 3]



   .. py:method:: give_emission_state(ob_stat, e_mat)

      Gives the emission matrix of observed states
      Return emission matrix [n_ref+1, n_loci] of each
      ob_stat: [2, n_loci] Matrix with Nr Ref/Alt Reads in Row0/Row1 (!)
      e_mat: Probabilities of genotypes [n_ref+1, n_loci, 3]



   .. py:method:: give_emission(ob_stat)

      Return the full emission Probability directly in Log Space.
      ob_stat: Observed Readcounts [2,l] array of 0/1



.. py:class:: Diploid_GT_Emissions(ref_haps=[])

   Bases: :py:obj:`RC_Model_Emissions`


   Implements the Emission probabilities for Diploid Genotype calls.
   Inherits top level Model_Emission, in particular the constructor (Calculation
   of Mean Allele Frequency from the Reference and ref_haps) and from
   RC_Model_Emission, in particular the calculation of probabilities of the
   [n_ref+1, n_loci, 3] genotype probability matrix give_emission_matrix


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



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



   .. py:attribute:: e_mat
      :value: []



   .. py:attribute:: e_rate
      :value: 0.001



   .. py:attribute:: e_rate_ref
      :value: 0.0



   .. py:method:: give_emission_state(ob_stat, e_mat)

      Gives the emission matrix of observed states
      Return emission matrix [n_ref+1, n_loci] of each
      ob_stat: [2, n_loci] Matrix with 0 or 1 for Ref or Alt
      e_mat: Probabilities of genotypes [n_ref+1, n_loci, 3]



   .. py:method:: give_emission(ob_stat, dtype=DTYPE)

      Return the full emission Probability directly in Log Space.
      ob_stat: Observed Readcounts [2,l] array of 0/1



.. py:class:: RC_Model_Emissions_withContamination(ref_haps=[], c=0.0, pCon=[])

   Bases: :py:obj:`RC_Model_Emissions`


   Implements the Read Count model Emission probabilities.
   Inherits from Model_Emission, in particular the constructor (Calculation
   of Mean Allele Frequency from the Reference and ref_haps)


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



   .. py:attribute:: emission_matrix
      :value: []



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



   .. py:method:: give_emission_matrix(remember=False)

      Return Emission Matrix, which describes
      probabilities in Genotypes [n_ref+1, n_loci, 3]



   .. py:method:: give_emission_state(ob_stat, e_mat)

      Gives the emission matrix of observed states
      Return emission matrix [n_ref+1, n_loci] of each
      ob_stat: [2, n_loci] Matrix with Nr Ref/Alt Reads in Row0/Row1 (!)
      e_mat: Probabilities of genotypes [n_ref+1, n_loci, 3]



   .. py:method:: give_emission(ob_stat)

      Return the full emission Probability directly in Log Space.
      ob_stat: Observed Readcounts [2,l] array of 0/1
      c: contamination rate



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

   Load the Emission Model


.. py:data:: ob_stat