#
# ChangeLog for / 
# 
# Generated by Trac 0.10.4
# 11/24/09 03:47:25
#


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

11/03/09 13:59:43 cholt [276]
	* data/te_proteins.fasta (modified)
	filtered te_protein file for low complexity proteins

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 21:45:45 bmoore [270]
	* bin/gff3_merge (modified)
	* bin/ipr_update_gff (modified)
	* bin/maker_functional_fasta (modified)
	* bin/maker_functional_gff (modified)
	* bin/maker_map_ids (modified)
	* bin/map_data_ids (added)
	* bin/map_fasta_ids (modified)
	Modifications to some scripts by Barry

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

09/22/09 14:31:50 cholt [267]
	* bin/maker2chado (modified)
	* perl/Install.PL (modified)
	small changes to make maker2chado fail when no chado

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

09/15/09 16:30:27 cholt [264]
	* Apollo/fly.tiers (deleted)
	remove old fly.tiers

09/15/09 16:29:51 cholt [263]
	* JBrowse (added)
	* JBrowse/genome.css (added)
	* JBrowse/maker_chado.json (added)
	* bin/maker2jbrowse (modified)
	include JBrowse configuration files

09/15/09 13:26:04 cholt [262]
	* bin/maker2jbrowse (modified)
	fix maker2jbrowse

09/14/09 13:13:04 cholt [261]
	* bin/maker2jbrowse (added)
	added maker2jbrowse

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 12:58:37 cholt [257]
	* bin/gff3_merge (modified)
	fix gff3_merge

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 13:47:56 cholt [253]
	* bin/maker2chado (modified)
	maker2chado use local libs

09/02/09 13:45:06 cholt [252]
	* lib/IO (added)
	* lib/IO/Prompt.pm (added)
	IO prompt

09/01/09 11:29:27 cholt [251]
	* bin/genemark_gtf2gff3 (added)
	added genemark gtf converter

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

08/13/09 14:34:20 cholt [241]
	* bin/maker2chado (added)
	maker2chado

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 16:02:36 cholt [238]
	* INSTALL (modified)
	INSTALL update

07/27/09 16:01:57 cholt [237]
	* lib/GI.pm (modified)
	GI updated

07/14/09 23:35:46 cholt [236]
	* MPI/mpi_maker (modified)
	* bin/maker (modified)
	fix usage

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 12:05:38 cholt [234]
	* bin/maker2zff.pl (modified)
	fix zff converter

07/14/09 12:01:22 cholt [233]
	* bin/maker2zff.pl (modified)
	fix zff converter

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 21:03:39 cholt [230]
	* Apollo/gff3.tiers (modified)
	updated gff3.tiers

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

07/07/09 15:18:54 cholt [227]
	* INSTALL (modified)
	* README (modified)
	* data/te_proteins.fasta (modified)
	fix documentation, fix te_proteins

06/22/09 17:04:45 cholt [226]
	* MPI/Install.PL (modified)
	updated intall

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 12:44:51 cholt [224]
	* MPI/mpi_iprscan (modified)
	* bin/fix_fasta (added)
	update mpi_iprscan

06/22/09 12:36:39 cholt [223]
	* bin/gff3_2_gbk (deleted)
	remove genbank converter

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

05/14/09 03:00:41 cholt [217]
	* bin/gff3_2_gbk (added)
	added genbank converter

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

05/06/09 13:03:22 bmoore [213]
	* bin/fasta_merge (modified)
	* bin/iprscan_batch (modified)
	minor changes to iprscan_batch and fasta_merge

05/04/09 16:40:07 cholt [212]
	* MPI/Install.PL (modified)
	* MPI/threads-1.71 (deleted)
	* perl/Install.PL (modified)
	* perl/threads-1.71 (added)
	* perl/threads-1.71/Changes (added)
	* perl/threads-1.71/MANIFEST (added)
	* perl/threads-1.71/META.yml (added)
	* perl/threads-1.71/Makefile.PL (added)
	* perl/threads-1.71/README (added)
	* perl/threads-1.71/examples (added)
	* perl/threads-1.71/examples/pool.pl (added)
	* perl/threads-1.71/hints (added)
	* perl/threads-1.71/hints/hpux.pl (added)
	* perl/threads-1.71/hints/linux.pl (added)
	* perl/threads-1.71/ppport.h (added)
	* perl/threads-1.71/t (added)
	* perl/threads-1.71/t/basic.t (added)
	* perl/threads-1.71/t/blocks.t (added)
	* perl/threads-1.71/t/context.t (added)
	* perl/threads-1.71/t/end.t (added)
	* perl/threads-1.71/t/err.t (added)
	* perl/threads-1.71/t/exit.t (added)
	* perl/threads-1.71/t/free.t (added)
	* perl/threads-1.71/t/free2.t (added)
	* perl/threads-1.71/t/join.t (added)
	* perl/threads-1.71/t/kill.t (added)
	* perl/threads-1.71/t/libc.t (added)
	* perl/threads-1.71/t/list.t (added)
	* perl/threads-1.71/t/pod.t (added)
	* perl/threads-1.71/t/problems.t (added)
	* perl/threads-1.71/t/stack.t (added)
	* perl/threads-1.71/t/stack_env.t (added)
	* perl/threads-1.71/t/state.t (added)
	* perl/threads-1.71/t/stress_cv.t (added)
	* perl/threads-1.71/t/stress_re.t (added)
	* perl/threads-1.71/t/stress_string.t (added)
	* perl/threads-1.71/t/test.pl (added)
	* perl/threads-1.71/t/thread.t (added)
	* perl/threads-1.71/threads.h (added)
	* perl/threads-1.71/threads.pm (added)
	* perl/threads-1.71/threads.xs (added)
	changed install process

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 19:21:50 bmoore [210]
	* MPI/mpi_maker (modified)
	Just a bit of whitespace cleanup on mpi_maker

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 14:59:45 cholt [208]
	* bin/iprscan_batch (modified)
	added usage to iprscan_batch

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

04/24/09 17:41:35 cholt [206]
	* README (modified)
	* bin/add_utr_gff.pl (modified)
	fix add_utr_gff

04/24/09 16:56:11 cholt [205]
	* bin/add_utr_gff.pl (modified)
	* bin/fasta_merge (modified)
	* bin/gff3_merge (modified)
	added lock control and other bug fixes

04/21/09 17:55:00 bmoore [204]
	* bin/ipr_update_gff (added)
	* bin/maker_functional_fasta (added)
	* bin/maker_functional_gff (added)
	added maker_functional_fasta maker_functional_gff ipr_update_gff

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

04/14/09 12:52:05 cholt [201]
	* bin/split_fasta (added)
	added split_fasta

04/13/09 16:52:41 hao [200]
	* lib/evaluator/pseudo_hit.pm (modified)
	fixed a bug in evaluator

04/10/09 12:00:34 bmoore [199]
	* README (modified)
	* bin/maker_map_ids (modified)
	* bin/map_fasta_ids (modified)
	* bin/map_gff_ids (modified)
	updates to ID mapping scripts and reformatted README for printer and
	screen

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 16:40:10 cholt [196]
	* bin/add_utr_start_stop_gff (added)
	* bin/gff3_2_gtf (added)
	* bin/iprscan2gff3 (added)
	* bin/iprscan_batch (added)
	commiting iprscan tools and gtf tools

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

04/04/09 12:26:02 bmoore [192]
	* bin/maker_map_ids (added)
	* bin/map_fasta_ids (added)
	* bin/map_gff_ids (added)
	Adding maker_map_ids, map_fasta_ids & map_gff_ids

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