-- generalize for new environment
-- mv Makefile to Makefile.sample -> changes to the Makefile are
	usually not of general interest
-- compute loss parameters for any input of eta1 and eta2
-- use new parameters for predictions, create segment graph also without reads -> quantification
-- simplify graph generation for known transcripts
Merge branch 'master' of github.com:ratschlab/MiTie
-- changing graph format to hdf5
-- write graphs as HDF5 files
-- split region into base and derived class
this way I dont need to include bam.h if I e.g. parse a gtf file