diff no work
add tophat scripts from Xintao
fix diff, add full STAR log
fix workflow generation script
fix bad merge in path
actually fix previous bug
remove bad test json
male se passes
add nthreads parameter
fix nthreads
add diff tophat
merge local
add bamUtil
initial rewrite of tophat-se
Merge remote-tracking branch 'origin/tophat_refactor' into local
update tophat scripts
update pe
try to set up real run
add some xintao scripts
Merge remote-tracking branch 'origin/tophat_refactor' into local