[Gmod-apollo-cmts] CVS: apollo/doc README.EnsJ, NONE, 1.1 todo, 1.841, NONE

[Brian O. <br...@us...>]

Update of /cvsroot/gmod/apollo/doc
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv19132

Added Files:
	README.EnsJ 
Removed Files:
	todo 
Log Message:
Remove todo, all items moved to Sourceforge or README

--- NEW FILE: README.EnsJ ---
$Id: README.EnsJ,v 1.1 2007/05/04 20:41:00 briano Exp $

Notes on various EnsJ issues.

Missing Databases
===================
The databases in the default history keep going away and then the EnsJ
adapter behaves badly and you have to hand-edit the default history and
maybe also ensj_defaults.conf (where is that used?).  There's got to be a
better way.

Stable IDs
===================
Stable IDs really are linked to DBs--should have a separate history
for each DB.

GFF Issue
===================
Load EnsJ, save as GFF, reload (using ensj.tiers)--nothing displayed!
GFF doesn't have any way to indicate that the genomic region doesn't
start at 1.  I guess that's a GFF deficiency rather than an EnsJ bug.

Stop and Start Don't Adjust
===================
Alex reported that stop and start don't adjust when moving splice
sites for ensj fugu. I found this to be true in ensj but couldnt
repeat in game.  [Not tested in new EnsJ adapter]

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