fixes for cluster
Merge branch 'master' of https://github.com/skillcoyne/IGCSA

Conflicts:
	ruby/read_sam_map.rb
Merge branch 'master' of https://github.com/skillcoyne/IGCSA
Merge branch 'master' of https://github.com/skillcoyne/IGCSA
Merge branch 'master' of https://github.com/skillcoyne/IGCSA
Merge branch 'master' of https://github.com/skillcoyne/IGCSA
Merge branch 'master' of https://github.com/skillcoyne/IGCSA
Merge branch 'master' of https://github.com/skillcoyne/IGCSA
Merge branch 'master' of https://github.com/skillcoyne/IGCSA
Merge branch 'master' of https://github.com/skillcoyne/IGCSA
Merge branch 'master' of https://github.com/skillcoyne/IGCSA
Merge branch 'master' of https://github.com/skillcoyne/IGCSA
fixed case where there are no reads