getWindows implemented
Merge branch 'master' of
https://github.com/pamelarussell/guttmanlab-core.git

Conflicts:
	src/annotationcollection/ConvertedSpace.java
fixed negative interval insert bug, incorrect size calculation bug
Corrected BED Reference Name
Merge branch 'master' of https://github.com/pamelarussell/guttmanlab-core.git