Widest path test code
Rewrote the fl_code to properly consider the experiment wide merginal distribution of fragment distributions, rather than the gene local counts.
Fixed an off by one error int eh expected fragment count code, and simplified the exon segment expression
Some refactoring
Removed the old peak calling code.
More refactoring
More refactoring
Added T*S nodes to the splice graph. Refactored so the transcript fragment iteration works directly off of the Splice graph.
Finished the element segment expresison rewrite - there are almost certianly still bugs.
Fixed a couple bugs, added more filters
Merge branch 'master' into widest_path
Merged README
Cleaned up merge
Fixed tiny merge conflict
Fixed a tiny bug
Merge branch 'master' into widest_path
Fixed a couple of bugs related to the merge
Ripped out some of the expensive element expression code.
Refactored the peak calling tuning parameter placement
Added PASSeq support to call_peaks. Also cleaned up the gene regions discovery code.