just started
added get_mean_tcn() and get_avail_cn()
added allocate_mean_tcn() and allocate_avail_cn()
emission.* clean
cloneHD.cpp clean
in cloneHD_functions()
cloneHD-functions.cpp clean
before going into clone.cpp
v1.16.7: fixed bugs in SNV+corr mode
fixed bug in Clone::trapezoidal()
Merge branch 'merge-source' into merge-target

Conflicts:
	cloneHD.cpp
mod get_maxcn_mask()
before factoring clone.pp
after factoring and new Makefile
moved source files to src
split off cloneHD-inference.cpp
added TODO
ordered clone.h
cleaned up cloneHD.cpp
clone.cpp clean