added check for input parameter setting
moved prune tag to also allow pruning for other strategies
sort introns by coordinate
Bug fix in insert intron edges

- missing check for empty index caused wrong node boundary to be
  introduced in splicing graph
Enforce closed intervals throughout code

- removed all the half-open / closed parts from the code
- sort event outputs by length
changed sort order of events and improved matching of alt end events while merging
Fixed bug in get_reads

- fixed length in MD field caused messed records when MD field had
  unexpected length
fixed that issue before on another branch
Merge branch 'master' of github.com:ratschlab/spladder

Resolved conflicts after merge

Conflicts:
	mex/Makefile
	src/gen_graphs.m