# # ChangeLog for /lib # # Generated by Trac 0.10.4 # 11/24/09 04:11:44 # 11/19/09 10:09:08 cholt [283] * MPI/mpi_iprscan (modified) * lib/iprscan/runlog.pm (modified) * lib/runlog.pm (modified) mpi_iprscan fixes 11/13/09 10:12:28 cholt [282] * lib/Widget/genemark/gmhmm_wrap (modified) fix gmhmm_wrap failure on overmasking bug 11/12/09 16:09:36 cholt [281] * bin/maker (modified) * lib/File/NFSLock.pm (modified) * lib/File/maintain.pl (added) * lib/GI.pm (modified) * lib/Widget/augustus.pm (modified) * lib/cluster.pm (modified) * lib/compare.pm (modified) * lib/evaluator/funs.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/runlog.pm (modified) no longer thread dependant, fixed overhang bug, and evidence clustering bug 11/10/09 12:27:50 bmoore [280] * lib/Widget/blastn.pm (modified) Minor tweak to an error message in lib/Widget/blastn.pm 11/10/09 12:26:01 bmoore [279] * bin/fasta_merge (modified) * bin/gff3_merge (modified) * lib/maker/auto_annotator.pm (modified) Carsons lib/maker/auto_annotator.pm update 11/04/09 15:48:01 cholt [278] * lib/Fasta.pm (modified) fix fasta parsing 11/04/09 09:39:38 cholt [277] * MPI/mpi_maker (modified) * bin/maker (modified) * lib/GI.pm (modified) * lib/PhatHit_utils.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Widget/exonerate/est2genome.pm (modified) * lib/runlog.pm (modified) attempt to fix exonerate holdover errors 10/12/09 14:06:24 cholt [275] * lib/GI.pm (modified) * lib/Widget/RepeatMasker.pm (modified) * lib/runlog.pm (modified) added some changes to how tmp is used and fixed blastrm params 10/11/09 00:43:34 cholt [274] * lib/GI.pm (modified) rm blastx but in parameters being passed 10/03/09 16:26:20 cholt [273] * lib/Widget/RepeatMasker.pm (modified) * lib/Widget/augustus.pm (modified) * lib/Widget/exonerate/est2genome.pm (modified) * lib/Widget/exonerate/protein2genome.pm (modified) * lib/Widget/snap.pm (modified) fix to check if snap, augustus, exonerate and RepeatMasker 10/03/09 11:41:34 cholt [272] * lib/runlog.pm (modified) fix runlog for lamorey 09/30/09 14:05:39 cholt [271] * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Widget/fgenesh.pm (modified) * lib/clean.pm (modified) * lib/ds_utility.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/runlog.pm (modified) make runlog softmask instensitive for old data. Fix fgenesh xdef errors 09/24/09 11:42:35 cholt [269] * lib/GI.pm (modified) * lib/ds_utility.pm (modified) * lib/runlog.pm (modified) try to fix weird randon cwd regular expression related error 09/23/09 11:23:55 cholt [268] * lib/GI.pm (modified) * lib/clean.pm (modified) * lib/cluster.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/runlog.pm (modified) added AED_threshold to MAKER 09/17/09 22:33:00 cholt [266] * lib/GI.pm (modified) undit filter=seg, unexpected problems 09/17/09 14:28:34 cholt [265] * lib/GI.pm (modified) set filter=seg for blastx instead of wordmask=seg, gives better performance 09/09/09 13:38:19 cholt [260] * lib/FastaDB.pm (modified) * lib/GI.pm (modified) * lib/PhatHit_utils.pm (modified) * lib/Widget/blastn.pm (modified) * lib/Widget/blastx.pm (modified) * lib/Widget/tblastx.pm (modified) made indexing search less IO intensive 09/08/09 16:43:05 cholt [259] * MPI/mpi_iprscan (modified) * lib/Process/IPRchunk.pm (modified) * lib/Process/MpiTiers.pm (modified) * lib/basiclog.pm (added) * lib/iprscan/runlog.pm (modified) mpi_iprscan more maker like behavior 09/08/09 11:32:56 cholt [258] * MPI/mpi_iprscan (modified) * lib/Process/IPRchunk.pm (modified) * lib/Process/MpiTiers.pm (modified) * lib/iprscan (added) * lib/iprscan/runlog.pm (added) better iprscan wrapper 09/04/09 10:45:29 cholt [256] * MPI/mpi_iprscan (modified) * MPI/mpi_maker (modified) * bin/maker (modified) * lib/Process/IPRchunk.pm (modified) * lib/Process/IPRtiers.pm (deleted) * lib/Process/MpiChunk.pm (modified) * lib/Process/MpiTiers.pm (modified) Update tiers 09/04/09 09:54:32 cholt [255] * lib/Process/MpiChunk.pm (modified) * lib/Process/MpiTiers.pm (modified) update how chunks and tiers work to accept chunk type 09/04/09 09:46:41 cholt [254] * bin/fasta_merge (modified) * bin/gff3_merge (modified) * lib/Process/IPRchunk.pm (modified) * lib/Process/IPRtiers.pm (modified) iprscan and gff3_merge and fasta__merge update 09/02/09 13:45:06 cholt [252] * lib/IO (added) * lib/IO/Prompt.pm (added) IO prompt 09/01/09 11:26:15 cholt [250] * lib/Process/MpiTiers.pm (modified) fix run_all method and next_chunk method in MpiTiers 08/31/09 17:07:51 cholt [249] * bin/maker (modified) * lib/FastaDB.pm (added) * lib/GI.pm (modified) * lib/Widget/RepeatMasker.pm (modified) * lib/Widget/blastn.pm (modified) * lib/Widget/blastx.pm (modified) * lib/Widget/tblastx.pm (modified) index error fixes 08/31/09 08:34:40 cholt [248] * lib/GI.pm (modified) * lib/Widget/blastn.pm (modified) * lib/Widget/blastx.pm (modified) * lib/Widget/tblastx.pm (modified) weird index error and blast merge error 08/27/09 12:41:35 cholt [247] * lib/GI.pm (modified) fix weird merging error 08/25/09 12:23:02 cholt [246] * lib/Widget/genemark.pm (modified) * lib/Widget/genemark/gmhmm_wrap (modified) fix genemark bug 08/24/09 17:03:49 cholt [245] * lib/Widget/fgenesh (added) * lib/Widget/fgenesh/fgenesh_wrap (added) fgenesh fix 08/21/09 16:52:11 cholt [244] * INSTALL (modified) * MPI/mpi_evaluator (modified) * MPI/mpi_maker (modified) * README (modified) * bin/maker (modified) * lib/GI.pm (modified) * lib/PhatHit_utils.pm (modified) * lib/Widget/fgenesh.pm (modified) * lib/Widget/genemark/gmhmm_wrap (modified) bug in repeat mask cause by prok upgrade 08/21/09 10:05:33 cholt [243] * lib/PhatHit_utils.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/runlog.pm (modified) prokaryote maker updae 08/18/09 14:25:27 cholt [242] * bin/maker2chado (modified) * lib/GI.pm (modified) * lib/PhatHit_utils.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Widget/genemark.pm (modified) * lib/Widget/genemark/gmhmm_wrap (added) * lib/Widget/genemark/gmhmme3_wrap (deleted) * lib/maker/auto_annotator.pm (modified) prokaryote maker 08/03/09 13:05:45 cholt [240] * lib/File/NFSLock.pm (modified) fix nfs lock 07/27/09 16:04:03 cholt [239] * lib/GI.pm (modified) GI updated 07/27/09 16:01:57 cholt [237] * lib/GI.pm (modified) GI updated 07/14/09 23:23:44 cholt [235] * bin/maker2zff.pl (modified) * lib/GI.pm (modified) * lib/maker/auto_annotator.pm (modified) fixed for abinit to pred_gff 07/14/09 11:37:18 cholt [232] * lib/GI.pm (modified) quick repeatmask 07/14/09 11:36:10 cholt [231] * lib/Widget/formatdb.pm (modified) fix formatdb 07/12/09 20:49:05 cholt [229] * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/runlog.pm (modified) gmod build 07/07/09 15:20:38 cholt [228] * MPI/mpi_iprscan (modified) * lib/Process/IPRtiers.pm (modified) * lib/shadow_AED.pm (modified) update mpi_iprscan 06/22/09 16:20:18 cholt [225] * MPI/mpi_iprscan (modified) * lib/Process/IPRchunk.pm (modified) * lib/Widget/iprscan.pm (modified) fix more mpi_iprscan 06/22/09 12:34:39 cholt [222] * bin/gff3_2_gtf (modified) * bin/maker2zff.pl (modified) * lib/GI.pm (modified) * lib/Widget/fgenesh.pm (modified) * lib/Widget/snap.pm (modified) * lib/exonerate/splice_info.pm (modified) * lib/runlog.pm (modified) update maker 06/22/09 12:33:44 cholt [221] * MPI/mpi_iprscan (added) * bin/add_utr_start_stop_gff (modified) * lib/Process/IPRchunk.pm (added) * lib/Process/IPRtiers.pm (added) * lib/Process/MpiChunk.pm (modified) * lib/Widget/iprscan.pm (added) * lib/basiclog.pm (added) mpi_iprscan added 06/12/09 16:57:31 hao [220] * lib/evaluator/AED.pm (modified) * lib/evaluator/evaluate.pm (modified) AED is corrected in evaluator and no more nearly infinite loop~ 06/12/09 15:55:52 hao [219] * lib/evaluator/AED.pm (modified) * lib/evaluator/pseudo_hit.pm (modified) greatly changed evaluator AED calculated algorithm to make it fasta, but still on the way of improving 06/03/09 11:46:38 hao [218] * lib/evaluator/evaluate.pm (modified) * lib/evaluator/fathom_utils.pm (modified) fixed an evaluator bug 05/13/09 09:32:23 cholt [216] * lib/Widget/augustus.pm (modified) augustus update 05/13/09 09:17:32 cholt [215] * lib/Widget/augustus.pm (modified) augustus fix 05/12/09 17:00:43 cholt [214] * lib/GFFDB.pm (modified) * lib/Widget/augustus.pm (modified) fix for new augustus output 04/30/09 14:02:43 cholt [211] * lib/Widget/genemark (added) * lib/Widget/genemark/gmhmme3_wrap (added) added better genemark support 04/28/09 15:01:45 cholt [209] * INSTALL (modified) * MPI/mpi_maker (modified) * README (modified) * lib/File/NFSLock.pm (modified) * lib/GI.pm (modified) * lib/ds_utility.pm (modified) * lib/runlog.pm (modified) lock file update 04/28/09 14:58:46 cholt [207] * lib/Widget/RepeatMasker.pm (modified) * lib/Widget/augustus.pm (modified) * lib/Widget/blastn.pm (modified) * lib/Widget/blastx.pm (modified) * lib/Widget/exonerate.pm (modified) * lib/Widget/fgenesh.pm (modified) * lib/Widget/formatdb.pm (modified) * lib/Widget/genemark.pm (modified) * lib/Widget/pressdb.pm (modified) * lib/Widget/setdb.pm (modified) * lib/Widget/snap.pm (modified) * lib/Widget/tblastx.pm (modified) * lib/Widget/xdformat.pm (modified) fix error checking in widgets 04/14/09 14:54:26 hao [203] * lib/evaluator/pseudo_hit.pm (modified) fixed a evaluator bug in pseudo_hit.pm 04/14/09 12:53:07 cholt [202] * bin/iprscan2gff3 (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GFFDB.pm (modified) * lib/maker/auto_annotator.pm (modified) fixed some gff3 issues 04/13/09 16:52:41 hao [200] * lib/evaluator/pseudo_hit.pm (modified) fixed a bug in evaluator 04/08/09 14:42:34 cholt [198] * MPI/Install.PL (modified) * MPI/mpi_evaluator (added) * MPI/mpi_maker (modified) * bin/evaluator (modified) * bin/maker (modified) * lib/GI.pm (modified) Changed back to three control files, and added mpi_evaluator 04/08/09 13:54:07 cholt [197] * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/runlog.pm (modified) mapping formard now works 04/07/09 16:36:40 cholt [195] * MPI/mpi_maker (modified) * bin/maker (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/runlog.pm (modified) fix dumper GFFDB, and added again option to maker 04/07/09 15:36:10 cholt [194] * bin/maker (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GFFDB.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/cluster.pm (modified) * lib/maker/auto_annotator.pm (modified) fix GFF dumper error, fix bad CDS error, fix change gffdb error, fix uniw gff name error, gffdb file locking now in place 04/04/09 12:43:21 cholt [193] * lib/maker/join.pm (modified) * lib/runlog.pm (modified) fix UTR join 04/02/09 00:18:17 cholt [191] * lib/runlog.pm (modified) fix run_log 04/01/09 23:40:44 cholt [190] * lib/runlog.pm (modified) improve runlog to always remove temp_dirs 04/01/09 23:32:59 cholt [189] * lib/runlog.pm (modified) fix run_log not deleting error 04/01/09 15:42:04 cholt [188] * bin/maker (modified) * lib/maker/auto_annotator.pm (modified) fix auto_annotator predictions not moving forward bug 04/01/09 14:59:13 cholt [187] * lib/maker/auto_annotator.pm (modified) fix auto_annotator bug 04/01/09 14:31:37 cholt [186] * lib/maker/auto_annotator.pm (modified) fix all_preds in evidence and changed how clusters are made for auto_annotator 03/31/09 16:14:50 cholt [185] * Apollo/gff3.tiers (modified) * lib/Process/MpiChunk.pm (modified) * lib/maker/auto_annotator.pm (modified) fix auto_annotator error and control files error and updarte gff3.tiers 03/31/09 15:38:02 cholt [184] * lib/GI.pm (modified) fix bug in control file proccessing 03/31/09 15:17:40 cholt [183] * bin/gff3_merge (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/maker/join.pm (modified) * lib/runlog.pm (modified) * lib/shadow_AED.pm (modified) map names forward, CDS competition on opposite strands accounted for 03/26/09 22:50:47 cholt [182] * Apollo/gff3.tiers (modified) * lib/Widget/augustus.pm (modified) * lib/runlog.pm (modified) augustus bug fix and gff3.tiers edit 03/26/09 16:44:29 cholt [181] * data/te_proteins.fasta (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/maker/auto_annotator.pm (modified) update maker to accept min protein lengths 03/25/09 11:14:17 cholt [179] * lib/GFFDB.pm (modified) temporary fix to GFFDB.pm names 03/24/09 15:08:16 cholt [173] * MPI/mpi_maker (modified) * README (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Widget/RepeatMasker.pm (modified) * lib/Widget/fgenesh.pm (modified) * lib/runlog.pm (modified) update README 03/23/09 23:09:11 cholt [172] * lib/Bio/Search/HSP/PhatHSP/genemark.pm (added) * lib/Bio/Search/Hit/PhatHit/genemark.pm (added) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Widget/genemark.pm (added) * lib/maker/auto_annotator.pm (modified) * lib/polisher/exonerate/est.pm (modified) * lib/polisher/exonerate/protein.pm (modified) * lib/runlog.pm (modified) added genemark 03/20/09 15:49:38 cholt [171] * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GI.pm (modified) added genemark 03/20/09 10:37:57 hao [170] * lib/evaluator/AED.pm (modified) fixed another bug in evaluator in passing parameters 03/19/09 17:09:08 cholt [169] * lib/maker/auto_annotator.pm (modified) fix evidence merge bug 03/19/09 16:55:49 cholt [168] * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Widget/augustus.pm (modified) * lib/Widget/fgenesh.pm (modified) * lib/Widget/snap.pm (modified) * lib/maker/auto_annotator.pm (modified) added check pn abinit overhang 03/19/09 15:38:00 hao [167] * lib/evaluator/evaluate.pm (modified) Fix a minor bug in evaluate.pm 03/18/09 14:45:05 cholt [166] * lib/Dumper/GFF/GFFV3.pm (modified) * lib/maker/auto_annotator.pm (modified) fix B < E error and many more 03/18/09 14:09:53 cholt [165] * lib/Dumper/GFF/GFFV3.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Process/MpiTiers.pm (modified) * lib/maker/auto_annotator.pm (modified) fix evidence merge error 03/17/09 17:15:26 cholt [164] * lib/maker/auto_annotator.pm (modified) fix gff3 passthrough error 03/17/09 16:33:56 cholt [163] * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GI.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/maker/join.pm (modified) * lib/shadow_AED.pm (modified) fix hsp duplication error 03/17/09 13:31:36 cholt [162] * bin/maker (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/evaluator/evaluate.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/runlog.pm (modified) evaluator ok to run in new maker 03/17/09 11:17:17 cholt [161] * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/maker/join.pm (modified) * lib/maker/quality_index.pm (modified) * lib/runlog.pm (modified) xAED implemented 03/16/09 14:18:16 cholt [160] * MPI/mpi_maker (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/maker/join.pm (modified) * lib/runlog.pm (modified) * lib/shadow_AED.pm (modified) Maker Updates for OOmycete genome, clone hsps, hits in join.pm 03/09/09 00:50:16 cholt [159] * MPI/mpi_maker (modified) * bin/fasta_merge (modified) * bin/gff3_preds2models (added) * bin/maker (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/File (added) * lib/File/NFSLock.pm (added) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Process/MpiTiers.pm (modified) * lib/Widget/RepeatMasker.pm (modified) * lib/Widget/fgenesh.pm (modified) * lib/cluster.pm (modified) * lib/evaluator/evaluate.pm (modified) * lib/runlog.pm (modified) maker update for all oomycete 03/09/09 00:49:43 cholt [158] * lib/maker/auto_annotator.pm (modified) maker update with oomycete genome 02/25/09 15:03:14 hao [157] * lib/GFFDB.pm (modified) * lib/evaluator/fathom_utils.pm (modified) 02/20/09 17:43:22 hao [156] * lib/evaluator/evaluate.pm (modified) * lib/maker/auto_annotator.pm (modified) Fix no evaluator output bug 02/20/09 13:55:44 cholt [155] * lib/evaluator/evaluate.pm (modified) * lib/maker/auto_annotator.pm (modified) fix fail on fathom disabled 02/20/09 13:40:05 cholt [153] * lib/GI.pm (modified) fathom enabled 02/20/09 12:42:04 cholt [152] * lib/maker/auto_annotator.pm (modified) evaluator active 02/20/09 12:38:14 cholt [151] * Apollo/gff3.tiers (modified) * MPI/mpi_maker (modified) * bin/gff3_merge (modified) * bin/maker (modified) * lib/Bio/Search/Hit/PhatHit/Base.pm (modified) * lib/CGL/TranslationMachine.pm (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/Fasta.pm (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Widget/augustus.pm (modified) * lib/clean.pm (modified) * lib/cluster.pm (modified) * lib/evaluator/funs.pm (modified) * lib/evaluator/quality_index.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/maker/join.pm (modified) * lib/shadow_AED.pm (modified) maker update CDS has stop codon and other opts 02/10/09 13:58:36 hao [150] * lib/evaluator/fathom_utils.pm (modified) 02/10/09 12:02:11 hao [147] * lib/evaluator/AED.pm (modified) * lib/evaluator/evaluate.pm (modified) * lib/evaluator/fathom_utils.pm (modified) * lib/evaluator/pseudo_hit.pm (modified) * lib/maker/auto_annotator.pm (modified) 02/09/09 16:49:11 cholt [146] * MPI/mpi_maker (modified) * bin/maker (modified) * lib/Dumper/GFF/GFFV3.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/evaluator/evaluate.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/shadow_AED.pm (added) temporarily disabled evaluator AED 02/07/09 00:29:07 cholt [145] * lib/GI.pm (modified) * lib/maker/auto_annotator.pm (modified) * lib/runlog.pm (modified) fix single exon est2genome error 02/06/09 23:23:19 cholt [144] * MPI/mpi_maker (modified) * bin/maker (modified) * bin/mpi_maker (deleted) * lib/FastaChunker.pm (modified) * lib/GFFDB.pm (modified) * lib/GI.pm (modified) * lib/Process/MpiChunk.pm (modified) * lib/Process/MpiTiers.pm (modified) mpi maker updated 02/06/09 17:02:43 cholt [143] * bin/maker (modified) * lib/Fasta.pm (modified) * lib/GI.pm (modified) * lib/Widget/fgenesh.pm (modified) fix weird fasta errors