hapsburg.func
=============

.. py:module:: hapsburg.func


Functions
---------

.. autoapisummary::

   hapsburg.func.fwd_bkwd_p
   hapsburg.func.viterbi_path_p
   hapsburg.func.sloppyROH_cumsum


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

.. py:function:: fwd_bkwd_p(e_prob0, t_mat, fwd, bwd, r_map)

   Takes emission and transition probabilities, and calculates posteriors.
   Input: [kxl] matrices of emission, transition
   and initialized fwd and bwd probabilities. All in log Space


.. py:function:: viterbi_path_p(e_prob0, t_mat0, end_p0)

   Implementation of a Viterbi Path.
   e_prob0 and t_mat0 [k,l] Matrices with Emission and Transition Probabilities.
   end_p: probability to begin/end in states [k]


.. py:function:: sloppyROH_cumsum(recoMap, target, refHaps, windowSize=0.001)

   Figure out per snp agreement between references and reads from target
   Return Max. fraction of reads agreeing with Ref Panel
   recoMap: Recombination Map [in Morgan] [l]
   target: Target Readcounts: [2, l]
   refHaps: Reference Haplotypes: [k, l]
   windowsize: Extension to each side [in M]