Merge branch 'development' of git://github.com/KonradZych/phenotypes2genotypes
correct handlig of a HT mode case

when offspring$phenotypes store a name of the file instead of the matrix
with phenotypes
stop -> cat

no need to stop here
stop -> cat and reformatting

no need to stop in here
bugfix

founders data should be read in that place
formatting
cleaning the code and new features

preparing for merging normal and HT mode
removing obsolete code
new features

correct handling of the HT mode EM
new features

checking for the variation in the row before EM
bugfix

stupid copy/paste bug
reformatting
reformatting
adding features

last piece of code to make new HT mode work
cleaning the code
cleaning and reformatting

putting duplicated code into the function
new way of handling HT reading
changing the binding of new rows
bugfix
bugfixes

minor