%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 
% starter for the varid wrapper varid_single.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 

% add paths.
addpath('tools')
addpath('VARiD')
addpath('VARiD_tools')
addpath('GUI')



% prepare parameters.

% path to the prettyprint readfile (Colorspace or Letterspace)
readsfile = 'D:/inputs/snd/mapped_1/NA17156_CS_10x_shrimp';
% path to the mfa or fa reference file
reffile = 'D:/inputs/snd/reffiles/R001.template.clean.PN.fa';
% name of the dataset/individual (to be printed in the prettybase output)
refname = 'NA17156';
% prepared path for storing temporary read files (this is preformed if the
% reference file has multiple references)
tmppath = 'D:/inputs/varid_out/single';
% threshold for the probability matrix resulting from the F-B run, for
% calling a position. In general, VARiD is not very sensitive to this
% value: anything around a high 90% will be good.
thr = 0.98;



% run varid. 
varid_single(readsfile, reffile, refname, thr, tmppath);
