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Rev Chgset Date Author Log Message
(edit) @278 [278] 11/04/2009 03:48:01 PM cholt fix fasta parsing
(edit) @277 [277] 11/04/2009 09:39:38 AM cholt attempt to fix exonerate holdover errors
(edit) @275 [275] 10/12/2009 02:06:24 PM cholt added some changes to how tmp is used and fixed blastrm params
(edit) @274 [274] 10/11/2009 12:43:34 AM cholt rm blastx but in parameters being passed
(edit) @273 [273] 10/03/2009 04:26:20 PM cholt fix to check if snap, augustus, exonerate and RepeatMasker?
(edit) @272 [272] 10/03/2009 11:41:34 AM cholt fix runlog for lamorey
(edit) @271 [271] 09/30/2009 02:05:39 PM cholt make runlog softmask instensitive for old data. Fix fgenesh xdef errors
(edit) @269 [269] 09/24/2009 11:42:35 AM cholt try to fix weird randon cwd regular expression related error
(edit) @268 [268] 09/23/2009 11:23:55 AM cholt added AED_threshold to MAKER
(edit) @266 [266] 09/17/2009 10:33:00 PM cholt undit filter=seg, unexpected problems
(edit) @265 [265] 09/17/2009 02:28:34 PM cholt set filter=seg for blastx instead of wordmask=seg, gives better …
(edit) @260 [260] 09/09/2009 01:38:19 PM cholt made indexing search less IO intensive
(edit) @259 [259] 09/08/2009 04:43:05 PM cholt mpi_iprscan more maker like behavior
(edit) @258 [258] 09/08/2009 11:32:56 AM cholt better iprscan wrapper
(edit) @256 [256] 09/04/2009 10:45:29 AM cholt Update tiers
(edit) @255 [255] 09/04/2009 09:54:32 AM cholt update how chunks and tiers work to accept chunk type
(edit) @254 [254] 09/04/2009 09:46:41 AM cholt iprscan and gff3_merge and fastamerge update
(edit) @252 [252] 09/02/2009 01:45:06 PM cholt IO prompt
(edit) @250 [250] 09/01/2009 11:26:15 AM cholt fix run_all method and next_chunk method in MpiTiers?
(edit) @249 [249] 08/31/2009 05:07:51 PM cholt index error fixes
(edit) @248 [248] 08/31/2009 08:34:40 AM cholt weird index error and blast merge error
(edit) @247 [247] 08/27/2009 12:41:35 PM cholt fix weird merging error
(edit) @246 [246] 08/25/2009 12:23:02 PM cholt fix genemark bug
(edit) @245 [245] 08/24/2009 05:03:49 PM cholt fgenesh fix
(edit) @244 [244] 08/21/2009 04:52:11 PM cholt bug in repeat mask cause by prok upgrade
(edit) @243 [243] 08/21/2009 10:05:33 AM cholt prokaryote maker updae
(edit) @242 [242] 08/18/2009 02:25:27 PM cholt prokaryote maker
(edit) @240 [240] 08/03/2009 01:05:45 PM cholt fix nfs lock
(edit) @239 [239] 07/27/2009 04:04:03 PM cholt GI updated
(edit) @237 [237] 07/27/2009 04:01:57 PM cholt GI updated
(edit) @235 [235] 07/14/2009 11:23:44 PM cholt fixed for abinit to pred_gff
(edit) @232 [232] 07/14/2009 11:37:18 AM cholt quick repeatmask
(edit) @231 [231] 07/14/2009 11:36:10 AM cholt fix formatdb
(edit) @229 [229] 07/12/2009 08:49:05 PM cholt gmod build
(edit) @228 [228] 07/07/2009 03:20:38 PM cholt update mpi_iprscan
(edit) @225 [225] 06/22/2009 04:20:18 PM cholt fix more mpi_iprscan
(edit) @222 [222] 06/22/2009 12:34:39 PM cholt update maker
(edit) @221 [221] 06/22/2009 12:33:44 PM cholt mpi_iprscan added
(edit) @220 [220] 06/12/2009 04:57:31 PM hao AED is corrected in evaluator and no more nearly infinite loop~
(edit) @219 [219] 06/12/2009 03:55:52 PM hao greatly changed evaluator AED calculated algorithm to make it fasta, but …
(edit) @218 [218] 06/03/2009 11:46:38 AM hao fixed an evaluator bug
(edit) @216 [216] 05/13/2009 09:32:23 AM cholt augustus update
(edit) @215 [215] 05/13/2009 09:17:32 AM cholt augustus fix
(edit) @214 [214] 05/12/2009 05:00:43 PM cholt fix for new augustus output
(edit) @211 [211] 04/30/2009 02:02:43 PM cholt added better genemark support
(edit) @209 [209] 04/28/2009 03:01:45 PM cholt lock file update
(edit) @207 [207] 04/28/2009 02:58:46 PM cholt fix error checking in widgets
(edit) @203 [203] 04/14/2009 02:54:26 PM hao fixed a evaluator bug in pseudo_hit.pm
(edit) @202 [202] 04/14/2009 12:53:07 PM cholt fixed some gff3 issues
(edit) @200 [200] 04/13/2009 04:52:41 PM hao fixed a bug in evaluator
(edit) @198 [198] 04/08/2009 02:42:34 PM cholt Changed back to three control files, and added mpi_evaluator
(edit) @197 [197] 04/08/2009 01:54:07 PM cholt mapping formard now works
(edit) @195 [195] 04/07/2009 04:36:40 PM cholt fix dumper GFFDB, and added again option to maker
(edit) @194 [194] 04/07/2009 03:36:10 PM cholt fix GFF dumper error, fix bad CDS error, fix change gffdb error, fix uniw …
(edit) @193 [193] 04/04/2009 12:43:21 PM cholt fix UTR join
(edit) @191 [191] 04/02/2009 12:18:17 AM cholt fix run_log
(edit) @190 [190] 04/01/2009 11:40:44 PM cholt improve runlog to always remove temp_dirs
(edit) @189 [189] 04/01/2009 11:32:59 PM cholt fix run_log not deleting error
(edit) @188 [188] 04/01/2009 03:42:04 PM cholt fix auto_annotator predictions not moving forward bug
(edit) @187 [187] 04/01/2009 02:59:13 PM cholt fix auto_annotator bug
(edit) @186 [186] 04/01/2009 02:31:37 PM cholt fix all_preds in evidence and changed how clusters are made for …
(edit) @185 [185] 03/31/2009 04:14:50 PM cholt fix auto_annotator error and control files error and updarte gff3.tiers
(edit) @184 [184] 03/31/2009 03:38:02 PM cholt fix bug in control file proccessing
(edit) @183 [183] 03/31/2009 03:17:40 PM cholt map names forward, CDS competition on opposite strands accounted for
(edit) @182 [182] 03/26/2009 10:50:47 PM cholt augustus bug fix and gff3.tiers edit
(edit) @181 [181] 03/26/2009 04:44:29 PM cholt update maker to accept min protein lengths
(edit) @179 [179] 03/25/2009 11:14:17 AM cholt temporary fix to GFFDB.pm names
(edit) @173 [173] 03/24/2009 03:08:16 PM cholt update README
(edit) @172 [172] 03/23/2009 11:09:11 PM cholt added genemark
(edit) @171 [171] 03/20/2009 03:49:38 PM cholt added genemark
(edit) @170 [170] 03/20/2009 10:37:57 AM hao fixed another bug in evaluator in passing parameters
(edit) @169 [169] 03/19/2009 05:09:08 PM cholt fix evidence merge bug
(edit) @168 [168] 03/19/2009 04:55:49 PM cholt added check pn abinit overhang
(edit) @167 [167] 03/19/2009 03:38:00 PM hao Fix a minor bug in evaluate.pm
(edit) @166 [166] 03/18/2009 02:45:05 PM cholt fix B < E error and many more
(edit) @165 [165] 03/18/2009 02:09:53 PM cholt fix evidence merge error
(edit) @164 [164] 03/17/2009 05:15:26 PM cholt fix gff3 passthrough error
(edit) @163 [163] 03/17/2009 04:33:56 PM cholt fix hsp duplication error
(edit) @162 [162] 03/17/2009 01:31:36 PM cholt evaluator ok to run in new maker
(edit) @161 [161] 03/17/2009 11:17:17 AM cholt xAED implemented
(edit) @160 [160] 03/16/2009 02:18:16 PM cholt Maker Updates for OOmycete genome, clone hsps, hits in join.pm
(edit) @159 [159] 03/09/2009 12:50:16 AM cholt maker update for all oomycete
(edit) @158 [158] 03/09/2009 12:49:43 AM cholt maker update with oomycete genome
(edit) @157 [157] 02/25/2009 03:03:14 PM hao --
(edit) @156 [156] 02/20/2009 05:43:22 PM hao Fix no evaluator output bug
(edit) @155 [155] 02/20/2009 01:55:44 PM cholt fix fail on fathom disabled
(edit) @153 [153] 02/20/2009 01:40:05 PM cholt fathom enabled
(edit) @152 [152] 02/20/2009 12:42:04 PM cholt evaluator active
(edit) @151 [151] 02/20/2009 12:38:14 PM cholt maker update CDS has stop codon and other opts
(edit) @150 [150] 02/10/2009 01:58:36 PM hao --
(edit) @147 [147] 02/10/2009 12:02:11 PM hao --
(edit) @146 [146] 02/09/2009 04:49:11 PM cholt temporarily disabled evaluator AED
(edit) @145 [145] 02/07/2009 12:29:07 AM cholt fix single exon est2genome error
(edit) @144 [144] 02/06/2009 11:23:19 PM cholt mpi maker updated
(edit) @143 [143] 02/06/2009 05:02:43 PM cholt fix weird fasta errors
(edit) @142 [142] 02/02/2009 05:48:46 PM hao removed UTR before generating snap-backwards
(edit) @141 [141] 02/02/2009 04:23:00 PM hao added snap-backwards score
(edit) @140 [140] 01/30/2009 02:40:35 PM hao --
(edit) @139 [139] 01/28/2009 12:54:41 PM cholt fix gff3 parsing error and blast empty error
(edit) @138 [138] 01/28/2009 10:43:01 AM hao --
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