Merge pull request #79 from wtangiit/master

add awe wrapper awe_blat.py
Merge pull request #80 from wtangiit/master

update in awe_preprocess.pl
Changed how parallel clustering files were being counted and named so that cluster ID's are no longer colliding.  Process number was not being updated correctly by python threads so that part was replaced.
Merge pull request #81 from jaredbischof/master

Fixed parallel clustering to provide unique cluster ID's
Temp filename was wrong when clustering with only 1 thread.
Merge pull request #82 from jaredbischof/master

Fixing temp filename.
Merge pull request #83 from wtangiit/master

update in awe_blat.py
Fixed bug where first cluster (if it was a singlet) was being printed twice.  Also, fixed bug where the last cluster was never being printed.  Finally, reconfigured the code so the logic was sane.
Added comments.
Added back line that's needed to ignore first empty line.
Merge pull request #84 from jaredbischof/master

Fixed bugs, added comments, and made more readable process_clusters script.
Merge pull request #85 from wtangiit/master

add awe wrappers for RNA related stages
Merge pull request #86 from wtangiit/master

add awe_rna_blat.sh, an alternate wrapper for stage 450 (blat+sort)