removed amoeba.d moved decodeStates into tools/. Started getSimStates.py
removed decodeStates from tools into separate project
changed cg Calling pipeline, added new scripts
added correct handling of multi-allelic sites in calling pipeline. Outputting only segregating sites in multihetsep
modified calling and phasing pipeline substantially
Merge branch 'dev' of github.com:stschiff/msmc into dev