Greg's changes to MakeRUMJunctionsFile
Change workflow to use sam file for junctions

Greg modified MakeRUMJunctionsFile so that it accepts a SAM
file as input, and uses that to derive junctions. I just
modified the pipeline so that it passes the SAM file into
MakeRUMJunctionsFile.
Use SAM file created by MakeRUMJunctionsFile

Greg modified MakeRUMJunctionsFile so that it writes a modified SAM
file out. I just changed the workflow so that we use that file.
Merge branch 'master' into sam2junctions
Working on integrating Greg's junciton script

Fixing tests for the new script
Fix tests for make_RUM_junction_file
Adding Greg's quantify_exons.pl script
Integrated Greg's new quantify_exons.pl script
Fix weird issue in SortRumByLocation

Some users reported getting errors when the script tries to
close a temporary file. Just warn when that happens; don't fail.