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Rev Chgset Date Author Log Message
(edit) @278 [278] 11/04/09 15:48:01 cholt fix fasta parsing
(edit) @277 [277] 11/04/09 09:39:38 cholt attempt to fix exonerate holdover errors
(edit) @276 [276] 11/03/09 13:59:43 cholt filtered te_protein file for low complexity proteins
(edit) @275 [275] 10/12/09 14:06:24 cholt added some changes to how tmp is used and fixed blastrm params
(edit) @274 [274] 10/11/09 00:43:34 cholt rm blastx but in parameters being passed
(edit) @273 [273] 10/03/09 16:26:20 cholt fix to check if snap, augustus, exonerate and RepeatMasker?
(edit) @272 [272] 10/03/09 11:41:34 cholt fix runlog for lamorey
(edit) @271 [271] 09/30/09 14:05:39 cholt make runlog softmask instensitive for old data. Fix fgenesh xdef errors
(edit) @270 [270] 09/24/09 21:45:45 bmoore Modifications to some scripts by Barry
(edit) @269 [269] 09/24/09 11:42:35 cholt try to fix weird randon cwd regular expression related error
(edit) @268 [268] 09/23/09 11:23:55 cholt added AED_threshold to MAKER
(edit) @267 [267] 09/22/09 14:31:50 cholt small changes to make maker2chado fail when no chado
(edit) @266 [266] 09/17/09 22:33:00 cholt undit filter=seg, unexpected problems
(edit) @265 [265] 09/17/09 14:28:34 cholt set filter=seg for blastx instead of wordmask=seg, gives better …
(edit) @264 [264] 09/15/09 16:30:27 cholt remove old fly.tiers
(edit) @263 [263] 09/15/09 16:29:51 cholt include JBrowse configuration files
(edit) @262 [262] 09/15/09 13:26:04 cholt fix maker2jbrowse
(edit) @261 [261] 09/14/09 13:13:04 cholt added maker2jbrowse
(edit) @260 [260] 09/09/09 13:38:19 cholt made indexing search less IO intensive
(edit) @259 [259] 09/08/09 16:43:05 cholt mpi_iprscan more maker like behavior
(edit) @258 [258] 09/08/09 11:32:56 cholt better iprscan wrapper
(edit) @257 [257] 09/04/09 12:58:37 cholt fix gff3_merge
(edit) @256 [256] 09/04/09 10:45:29 cholt Update tiers
(edit) @255 [255] 09/04/09 09:54:32 cholt update how chunks and tiers work to accept chunk type
(edit) @254 [254] 09/04/09 09:46:41 cholt iprscan and gff3_merge and fastamerge update
(edit) @253 [253] 09/02/09 13:47:56 cholt maker2chado use local libs
(edit) @252 [252] 09/02/09 13:45:06 cholt IO prompt
(edit) @251 [251] 09/01/09 11:29:27 cholt added genemark gtf converter
(edit) @250 [250] 09/01/09 11:26:15 cholt fix run_all method and next_chunk method in MpiTiers?
(edit) @249 [249] 08/31/09 17:07:51 cholt index error fixes
(edit) @248 [248] 08/31/09 08:34:40 cholt weird index error and blast merge error
(edit) @247 [247] 08/27/09 12:41:35 cholt fix weird merging error
(edit) @246 [246] 08/25/09 12:23:02 cholt fix genemark bug
(edit) @245 [245] 08/24/09 17:03:49 cholt fgenesh fix
(edit) @244 [244] 08/21/09 16:52:11 cholt bug in repeat mask cause by prok upgrade
(edit) @243 [243] 08/21/09 10:05:33 cholt prokaryote maker updae
(edit) @242 [242] 08/18/09 14:25:27 cholt prokaryote maker
(edit) @241 [241] 08/13/09 14:34:20 cholt maker2chado
(edit) @240 [240] 08/03/09 13:05:45 cholt fix nfs lock
(edit) @239 [239] 07/27/09 16:04:03 cholt GI updated
(edit) @238 [238] 07/27/09 16:02:36 cholt INSTALL update
(edit) @237 [237] 07/27/09 16:01:57 cholt GI updated
(edit) @236 [236] 07/14/09 23:35:46 cholt fix usage
(edit) @235 [235] 07/14/09 23:23:44 cholt fixed for abinit to pred_gff
(edit) @234 [234] 07/14/09 12:05:38 cholt fix zff converter
(edit) @233 [233] 07/14/09 12:01:22 cholt fix zff converter
(edit) @232 [232] 07/14/09 11:37:18 cholt quick repeatmask
(edit) @231 [231] 07/14/09 11:36:10 cholt fix formatdb
(edit) @230 [230] 07/12/09 21:03:39 cholt updated gff3.tiers
(edit) @229 [229] 07/12/09 20:49:05 cholt gmod build
(edit) @228 [228] 07/07/09 15:20:38 cholt update mpi_iprscan
(edit) @227 [227] 07/07/09 15:18:54 cholt fix documentation, fix te_proteins
(edit) @226 [226] 06/22/09 17:04:45 cholt updated intall
(edit) @225 [225] 06/22/09 16:20:18 cholt fix more mpi_iprscan
(edit) @224 [224] 06/22/09 12:44:51 cholt update mpi_iprscan
(edit) @223 [223] 06/22/09 12:36:39 cholt remove genbank converter
(edit) @222 [222] 06/22/09 12:34:39 cholt update maker
(edit) @221 [221] 06/22/09 12:33:44 cholt mpi_iprscan added
(edit) @220 [220] 06/12/09 16:57:31 hao AED is corrected in evaluator and no more nearly infinite loop~
(edit) @219 [219] 06/12/09 15:55:52 hao greatly changed evaluator AED calculated algorithm to make it fasta, but …
(edit) @218 [218] 06/03/09 11:46:38 hao fixed an evaluator bug
(edit) @217 [217] 05/14/09 03:00:41 cholt added genbank converter
(edit) @216 [216] 05/13/09 09:32:23 cholt augustus update
(edit) @215 [215] 05/13/09 09:17:32 cholt augustus fix
(edit) @214 [214] 05/12/09 17:00:43 cholt fix for new augustus output
(edit) @213 [213] 05/06/09 13:03:22 bmoore minor changes to iprscan_batch and fasta_merge
(edit) @212 [212] 05/04/09 16:40:07 cholt changed install process
(edit) @211 [211] 04/30/09 14:02:43 cholt added better genemark support
(edit) @210 [210] 04/28/09 19:21:50 bmoore Just a bit of whitespace cleanup on mpi_maker
(edit) @209 [209] 04/28/09 15:01:45 cholt lock file update
(edit) @208 [208] 04/28/09 14:59:45 cholt added usage to iprscan_batch
(edit) @207 [207] 04/28/09 14:58:46 cholt fix error checking in widgets
(edit) @206 [206] 04/24/09 17:41:35 cholt fix add_utr_gff
(edit) @205 [205] 04/24/09 16:56:11 cholt added lock control and other bug fixes
(edit) @204 [204] 04/21/09 17:55:00 bmoore added maker_functional_fasta maker_functional_gff ipr_update_gff
(edit) @203 [203] 04/14/09 14:54:26 hao fixed a evaluator bug in pseudo_hit.pm
(edit) @202 [202] 04/14/09 12:53:07 cholt fixed some gff3 issues
(edit) @201 [201] 04/14/09 12:52:05 cholt added split_fasta
(edit) @200 [200] 04/13/09 16:52:41 hao fixed a bug in evaluator
(edit) @199 [199] 04/10/09 12:00:34 bmoore updates to ID mapping scripts and reformatted README for printer and …
(edit) @198 [198] 04/08/09 14:42:34 cholt Changed back to three control files, and added mpi_evaluator
(edit) @197 [197] 04/08/09 13:54:07 cholt mapping formard now works
(edit) @196 [196] 04/07/09 16:40:10 cholt commiting iprscan tools and gtf tools
(edit) @195 [195] 04/07/09 16:36:40 cholt fix dumper GFFDB, and added again option to maker
(edit) @194 [194] 04/07/09 15:36:10 cholt fix GFF dumper error, fix bad CDS error, fix change gffdb error, fix uniw …
(edit) @193 [193] 04/04/09 12:43:21 cholt fix UTR join
(edit) @192 [192] 04/04/09 12:26:02 bmoore Adding maker_map_ids, map_fasta_ids & map_gff_ids
(edit) @191 [191] 04/02/09 00:18:17 cholt fix run_log
(edit) @190 [190] 04/01/09 23:40:44 cholt improve runlog to always remove temp_dirs
(edit) @189 [189] 04/01/09 23:32:59 cholt fix run_log not deleting error
(edit) @188 [188] 04/01/09 15:42:04 cholt fix auto_annotator predictions not moving forward bug
(edit) @187 [187] 04/01/09 14:59:13 cholt fix auto_annotator bug
(edit) @186 [186] 04/01/09 14:31:37 cholt fix all_preds in evidence and changed how clusters are made for …
(edit) @185 [185] 03/31/09 16:14:50 cholt fix auto_annotator error and control files error and updarte gff3.tiers
(edit) @184 [184] 03/31/09 15:38:02 cholt fix bug in control file proccessing
(edit) @183 [183] 03/31/09 15:17:40 cholt map names forward, CDS competition on opposite strands accounted for
(edit) @182 [182] 03/26/09 22:50:47 cholt augustus bug fix and gff3.tiers edit
(edit) @181 [181] 03/26/09 16:44:29 cholt update maker to accept min protein lengths
(edit) @180 [180] 03/25/09 11:19:22 cholt update documentation
(edit) @179 [179] 03/25/09 11:14:17 cholt temporary fix to GFFDB.pm names
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