First rewrite commit.
Added cluster gene finder - doesnt really work so reverting.
Reverted to the old gene discovery method, still not happy.
Reversion to the initial version. Still not super happy that this takes so long, might try to just cluster around the poly(a) sites.
More work, too slow, going to try a differnt approach.
Working version of gene finder.
Finished the exon rewrite.
A couple bug fixes.
Added rampage support.
Small changes.
Fixed major bug in TSS exon detection.
Added code to automatically clean chrm names for bam fetches.
Added fix for sparse genes.
Merge branch 'rewrite_cleanup' of wotan.lbl.gov:/srv/git/grit into rewrite_cleanup
Added code to find protein coding domains.
Made find elements multithreaded.
Merge remote-tracking branch 'origin/rewrite_cleanup' into rewrite_cleanup
Start of the integrated transcript enumeration.
Added some necessary files
Finished the RNAseq migration. Still ned to unify the fragment length estimation and CAGE/RAMPAGE support.