#
# ChangeLog for /bin 
# 
# Generated by Trac 0.10.4
# 11/24/09 04:19:18
#


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 12:26:01 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 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

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

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

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

09/04/09 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 09:46:41 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

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

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

08/21/09 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

08/18/09 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

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

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

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

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

04/28/09 14:59:45 cholt [208]
	* bin/iprscan_batch (modified)
	added usage to iprscan_batch

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 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

04/10/09 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

04/07/09 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 12:26:02 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

04/01/09 15:42:04 cholt [188]
	* bin/maker (modified)
	* lib/maker/auto_annotator.pm (modified)
	fix auto_annotator predictions not moving forward bug

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

03/25/09 10:52:13 cholt [176]
	* MPI/mpi_maker (modified)
	* bin/maker (modified)
	update use lib in maker

03/25/09 10:37:38 cholt [174]
	* INSTALL (modified)
	* README (modified)
	* bin/maker (modified)
	* perl (added)
	* perl/DBD-SQLite-0.31 (added)
	* perl/DBD-SQLite-0.31/Changes (added)
	* perl/DBD-SQLite-0.31/MANIFEST (added)
	* perl/DBD-SQLite-0.31/MANIFEST.SKIP (added)
	* perl/DBD-SQLite-0.31/META.yml (added)
	* perl/DBD-SQLite-0.31/Makefile.PL (added)
	* perl/DBD-SQLite-0.31/README (added)
	* perl/DBD-SQLite-0.31/SQLite.xs (added)
	* perl/DBD-SQLite-0.31/SQLiteXS.h (added)
	* perl/DBD-SQLite-0.31/attach.c (added)
	* perl/DBD-SQLite-0.31/auth.c (added)
	* perl/DBD-SQLite-0.31/btree.c (added)
	* perl/DBD-SQLite-0.31/btree.h (added)
	* perl/DBD-SQLite-0.31/btree_rb.c (added)
	* perl/DBD-SQLite-0.31/build.c (added)
	* perl/DBD-SQLite-0.31/copy.c (added)
	* perl/DBD-SQLite-0.31/date.c (added)
	* perl/DBD-SQLite-0.31/dbdimp.c (added)
	* perl/DBD-SQLite-0.31/dbdimp.h (added)
	* perl/DBD-SQLite-0.31/delete.c (added)
	* perl/DBD-SQLite-0.31/encode.c (added)
	* perl/DBD-SQLite-0.31/expr.c (added)
	* perl/DBD-SQLite-0.31/func.c (added)
	* perl/DBD-SQLite-0.31/getsqlite.pl (added)
	* perl/DBD-SQLite-0.31/hash.c (added)
	* perl/DBD-SQLite-0.31/hash.h (added)
	* perl/DBD-SQLite-0.31/insert.c (added)
	* perl/DBD-SQLite-0.31/lib (added)
	* perl/DBD-SQLite-0.31/lib/DBD (added)
	* perl/DBD-SQLite-0.31/lib/DBD/SQLite.pm (added)
	* perl/DBD-SQLite-0.31/main.c (added)
	* perl/DBD-SQLite-0.31/opcodes.c (added)
	* perl/DBD-SQLite-0.31/opcodes.h (added)
	* perl/DBD-SQLite-0.31/os.c (added)
	* perl/DBD-SQLite-0.31/os.h (added)
	* perl/DBD-SQLite-0.31/pager.c (added)
	* perl/DBD-SQLite-0.31/pager.h (added)
	* perl/DBD-SQLite-0.31/parse.c (added)
	* perl/DBD-SQLite-0.31/parse.h (added)
	* perl/DBD-SQLite-0.31/pragma.c (added)
	* perl/DBD-SQLite-0.31/printf.c (added)
	* perl/DBD-SQLite-0.31/random.c (added)
	* perl/DBD-SQLite-0.31/select.c (added)
	* perl/DBD-SQLite-0.31/sqlite.h (added)
	* perl/DBD-SQLite-0.31/sqliteInt.h (added)
	* perl/DBD-SQLite-0.31/t (added)
	* perl/DBD-SQLite-0.31/t/00basic.t (added)
	* perl/DBD-SQLite-0.31/t/01logon.t (added)
	* perl/DBD-SQLite-0.31/t/02cr_table.t (added)
	* perl/DBD-SQLite-0.31/t/03insert.t (added)
	* perl/DBD-SQLite-0.31/t/04select.t (added)
	* perl/DBD-SQLite-0.31/t/05tran.t (added)
	* perl/DBD-SQLite-0.31/t/06error.t (added)
	* perl/DBD-SQLite-0.31/t/08create_function.t (added)
	* perl/DBD-SQLite-0.31/t/09create_aggregate.t (added)
	* perl/DBD-SQLite-0.31/t/10dsnlist.t (added)
	* perl/DBD-SQLite-0.31/t/20createdrop.t (added)
	* perl/DBD-SQLite-0.31/t/30insertfetch.t (added)
	* perl/DBD-SQLite-0.31/t/40bindparam.t (added)
	* perl/DBD-SQLite-0.31/t/40blobs.t (added)
	* perl/DBD-SQLite-0.31/t/40listfields.t (added)
	* perl/DBD-SQLite-0.31/t/40nulls.t (added)
	* perl/DBD-SQLite-0.31/t/40numrows.t (added)
	* perl/DBD-SQLite-0.31/t/50chopblanks.t (added)
	* perl/DBD-SQLite-0.31/t/50commit.t (added)
	* perl/DBD-SQLite-0.31/t/60metadata.t (added)
	* perl/DBD-SQLite-0.31/t/90cppcomments.t (added)
	* perl/DBD-SQLite-0.31/t/99cleanup.t (added)
	* perl/DBD-SQLite-0.31/t/SQLite.dbtest (added)
	* perl/DBD-SQLite-0.31/t/ak-dbd.t (added)
	* perl/DBD-SQLite-0.31/t/dbdadmin.t (added)
	* perl/DBD-SQLite-0.31/t/lib.pl (added)
	* perl/DBD-SQLite-0.31/table.c (added)
	* perl/DBD-SQLite-0.31/tokenize.c (added)
	* perl/DBD-SQLite-0.31/trigger.c (added)
	* perl/DBD-SQLite-0.31/update.c (added)
	* perl/DBD-SQLite-0.31/util.c (added)
	* perl/DBD-SQLite-0.31/vacuum.c (added)
	* perl/DBD-SQLite-0.31/vdbe.c (added)
	* perl/DBD-SQLite-0.31/vdbe.h (added)
	* perl/DBD-SQLite-0.31/vdbeInt.h (added)
	* perl/DBD-SQLite-0.31/vdbeaux.c (added)
	* perl/DBD-SQLite-0.31/where.c (added)
	* perl/DBI-1.607 (added)
	* perl/DBI-1.607/Changes (added)
	* perl/DBI-1.607/DBI.pm (added)
	* perl/DBI-1.607/DBI.xs (added)
	* perl/DBI-1.607/DBIXS.h (added)
	* perl/DBI-1.607/Driver.xst (added)
	* perl/DBI-1.607/Driver_xst.h (added)
	* perl/DBI-1.607/MANIFEST (added)
	* perl/DBI-1.607/META.yml (added)
	* perl/DBI-1.607/Makefile.PL (added)
	* perl/DBI-1.607/Perl.xs (added)
	* perl/DBI-1.607/README (added)
	* perl/DBI-1.607/Roadmap.pod (added)
	* perl/DBI-1.607/TASKS.pod (added)
	* perl/DBI-1.607/TODO_2005.txt (added)
	* perl/DBI-1.607/dbd_xsh.h (added)
	* perl/DBI-1.607/dbi_sql.h (added)
	* perl/DBI-1.607/dbilogstrip.PL (added)
	* perl/DBI-1.607/dbipport.h (added)
	* perl/DBI-1.607/dbiprof.PL (added)
	* perl/DBI-1.607/dbiproxy.PL (added)
	* perl/DBI-1.607/dbivport.h (added)
	* perl/DBI-1.607/dbixs_rev.h (added)
	* perl/DBI-1.607/dbixs_rev.pl (added)
	* perl/DBI-1.607/ex (added)
	* perl/DBI-1.607/ex/perl_dbi_nulls_test.pl (added)
	* perl/DBI-1.607/ex/profile.pl (added)
	* perl/DBI-1.607/lib (added)
	* perl/DBI-1.607/lib/Bundle (added)
	* perl/DBI-1.607/lib/Bundle/DBI.pm (added)
	* perl/DBI-1.607/lib/DBD (added)
	* perl/DBI-1.607/lib/DBD/DBM.pm (added)
	* perl/DBI-1.607/lib/DBD/ExampleP.pm (added)
	* perl/DBI-1.607/lib/DBD/File.pm (added)
	* perl/DBI-1.607/lib/DBD/Gofer (added)
	* perl/DBI-1.607/lib/DBD/Gofer.pm (added)
	* perl/DBI-1.607/lib/DBD/Gofer/Policy (added)
	* perl/DBI-1.607/lib/DBD/Gofer/Policy/Base.pm (added)
	* perl/DBI-1.607/lib/DBD/Gofer/Policy/classic.pm (added)
	* perl/DBI-1.607/lib/DBD/Gofer/Policy/pedantic.pm (added)
	* perl/DBI-1.607/lib/DBD/Gofer/Policy/rush.pm (added)
	* perl/DBI-1.607/lib/DBD/Gofer/Transport (added)
	* perl/DBI-1.607/lib/DBD/Gofer/Transport/Base.pm (added)
	* perl/DBI-1.607/lib/DBD/Gofer/Transport/null.pm (added)
	* perl/DBI-1.607/lib/DBD/Gofer/Transport/pipeone.pm (added)
	* perl/DBI-1.607/lib/DBD/Gofer/Transport/stream.pm (added)
	* perl/DBI-1.607/lib/DBD/NullP.pm (added)
	* perl/DBI-1.607/lib/DBD/Proxy.pm (added)
	* perl/DBI-1.607/lib/DBD/Sponge.pm (added)
	* perl/DBI-1.607/lib/DBI (added)
	* perl/DBI-1.607/lib/DBI/Const (added)
	* perl/DBI-1.607/lib/DBI/Const/GetInfo (added)
	* perl/DBI-1.607/lib/DBI/Const/GetInfo/ANSI.pm (added)
	* perl/DBI-1.607/lib/DBI/Const/GetInfo/ODBC.pm (added)
	* perl/DBI-1.607/lib/DBI/Const/GetInfoReturn.pm (added)
	* perl/DBI-1.607/lib/DBI/Const/GetInfoType.pm (added)
	* perl/DBI-1.607/lib/DBI/DBD (added)
	* perl/DBI-1.607/lib/DBI/DBD.pm (added)
	* perl/DBI-1.607/lib/DBI/DBD/Metadata.pm (added)
	* perl/DBI-1.607/lib/DBI/FAQ.pm (added)
	* perl/DBI-1.607/lib/DBI/Gofer (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Execute.pm (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Request.pm (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Response.pm (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Serializer (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Serializer/Base.pm (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Serializer/DataDumper.pm (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Serializer/Storable.pm (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Transport (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Transport/Base.pm (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Transport/pipeone.pm (added)
	* perl/DBI-1.607/lib/DBI/Gofer/Transport/stream.pm (added)
	* perl/DBI-1.607/lib/DBI/Profile.pm (added)
	* perl/DBI-1.607/lib/DBI/ProfileData.pm (added)
	* perl/DBI-1.607/lib/DBI/ProfileDumper (added)
	* perl/DBI-1.607/lib/DBI/ProfileDumper.pm (added)
	* perl/DBI-1.607/lib/DBI/ProfileDumper/Apache.pm (added)
	* perl/DBI-1.607/lib/DBI/ProfileSubs.pm (added)
	* perl/DBI-1.607/lib/DBI/ProxyServer.pm (added)
	* perl/DBI-1.607/lib/DBI/PurePerl.pm (added)
	* perl/DBI-1.607/lib/DBI/SQL (added)
	* perl/DBI-1.607/lib/DBI/SQL/Nano.pm (added)
	* perl/DBI-1.607/lib/DBI/Util (added)
	* perl/DBI-1.607/lib/DBI/Util/CacheMemory.pm (added)
	* perl/DBI-1.607/lib/DBI/Util/_accessor.pm (added)
	* perl/DBI-1.607/lib/DBI/W32ODBC.pm (added)
	* perl/DBI-1.607/lib/Win32 (added)
	* perl/DBI-1.607/lib/Win32/DBIODBC.pm (added)
	* perl/DBI-1.607/t (added)
	* perl/DBI-1.607/t/01basics.t (added)
	* perl/DBI-1.607/t/02dbidrv.t (added)
	* perl/DBI-1.607/t/03handle.t (added)
	* perl/DBI-1.607/t/04mods.t (added)
	* perl/DBI-1.607/t/05concathash.t (added)
	* perl/DBI-1.607/t/06attrs.t (added)
	* perl/DBI-1.607/t/07kids.t (added)
	* perl/DBI-1.607/t/08keeperr.t (added)
	* perl/DBI-1.607/t/09trace.t (added)
	* perl/DBI-1.607/t/10examp.t (added)
	* perl/DBI-1.607/t/11fetch.t (added)
	* perl/DBI-1.607/t/12quote.t (added)
	* perl/DBI-1.607/t/13taint.t (added)
	* perl/DBI-1.607/t/14utf8.t (added)
	* perl/DBI-1.607/t/15array.t (added)
	* perl/DBI-1.607/t/19fhtrace.t (added)
	* perl/DBI-1.607/t/20meta.t (added)
	* perl/DBI-1.607/t/30subclass.t (added)
	* perl/DBI-1.607/t/35thrclone.t (added)
	* perl/DBI-1.607/t/40profile.t (added)
	* perl/DBI-1.607/t/41prof_dump.t (added)
	* perl/DBI-1.607/t/42prof_data.t (added)
	* perl/DBI-1.607/t/43prof_env.t (added)
	* perl/DBI-1.607/t/50dbm.t (added)
	* perl/DBI-1.607/t/60preparse.t (added)
	* perl/DBI-1.607/t/65transact.t (added)
	* perl/DBI-1.607/t/70callbacks.t (added)
	* perl/DBI-1.607/t/72childhandles.t (added)
	* perl/DBI-1.607/t/80proxy.t (added)
	* perl/DBI-1.607/t/85gofer.t (added)
	* perl/DBI-1.607/t/86gofer_fail.t (added)
	* perl/DBI-1.607/t/87gofer_cache.t (added)
	* perl/DBI-1.607/t/pod-coverage.t (added)
	* perl/DBI-1.607/t/pod.t (added)
	* perl/DBI-1.607/test.pl (added)
	* perl/DBI-1.607/typemap (added)
	* perl/Install.PL (added)
	added DBI and DBD::SQLite

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

03/09/09 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

02/20/09 13:42:57 cholt [154]
	* bin/fasta_merge (added)
	fasta_merge added

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

02/09/09 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

02/06/09 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

01/25/09 11:32:42 hao [134]
	* bin/maker (modified)
	* lib/evaluator/AED.pm (modified)
	* lib/evaluator/evaluate.pm (modified)
	Added new AED feature

01/23/09 16:22:26 cholt [131]
	* bin/maker (modified)
	* lib/GI.pm (modified)
	* lib/maker/auto_annotator.pm (modified)
	* lib/runlog.pm (modified)
	fix fasta index error

01/23/09 12:58:16 cholt [127]
	* MPI/threads-1.71/Makefile (added)
	* MPI/threads-1.71/blib (added)
	* MPI/threads-1.71/blib/arch (added)
	* MPI/threads-1.71/blib/arch/.exists (added)
	* MPI/threads-1.71/blib/arch/auto (added)
	* MPI/threads-1.71/blib/arch/auto/threads (added)
	* MPI/threads-1.71/blib/arch/auto/threads/.exists (added)
	* MPI/threads-1.71/blib/arch/auto/threads/threads.bs (added)
	* MPI/threads-1.71/blib/arch/auto/threads/threads.bundle (added)
	* MPI/threads-1.71/blib/bin (added)
	* MPI/threads-1.71/blib/bin/.exists (added)
	* MPI/threads-1.71/blib/lib (added)
	* MPI/threads-1.71/blib/lib/.exists (added)
	* MPI/threads-1.71/blib/lib/auto (added)
	* MPI/threads-1.71/blib/lib/auto/threads (added)
	* MPI/threads-1.71/blib/lib/auto/threads/.exists (added)
	* MPI/threads-1.71/blib/lib/threads.pm (added)
	* MPI/threads-1.71/blib/man1 (added)
	* MPI/threads-1.71/blib/man1/.exists (added)
	* MPI/threads-1.71/blib/man3 (added)
	* MPI/threads-1.71/blib/man3/.exists (added)
	* MPI/threads-1.71/blib/script (added)
	* MPI/threads-1.71/blib/script/.exists (added)
	* MPI/threads-1.71/pm_to_blib (added)
	* MPI/threads-1.71/threads.bs (added)
	* bin/add_utr_gff (deleted)
	* bin/add_utr_gff.pl (added)
	* bin/evaluator (added)
	* bin/gff3_merge (modified)
	* bin/maker (modified)
	* bin/maker2zff (deleted)
	* bin/maker2zff.pl (added)
	* bin/mpi_maker (added)
	* bin/split_fasta (deleted)
	* lib/Bio/Search/HSP/PhatHSP/Base.pm (modified)
	* lib/Bio/Search/HSP/PhatHSP/augustus.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/est2genome.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/fgenesh.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/gff3.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/protein2genome.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/repeatmasker.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/snap.pm (added)
	* lib/Bio/Search/Hit/PhatHit/Base.pm (modified)
	* lib/Bio/Search/Hit/PhatHit/augustus.pm (added)
	* lib/Bio/Search/Hit/PhatHit/est2genome.pm (added)
	* lib/Bio/Search/Hit/PhatHit/fgenesh.pm (added)
	* lib/Bio/Search/Hit/PhatHit/gff3.pm (added)
	* lib/Bio/Search/Hit/PhatHit/protein2genome.pm (added)
	* lib/Bio/Search/Hit/PhatHit/repeatmasker.pm (added)
	* lib/Bio/Search/Hit/PhatHit/snap.pm (added)
	* lib/Datastore/docs (deleted)
	* lib/Dumper/GFF/GFF3.pm (deleted)
	* lib/Dumper/GFF/GFF3_DEF.pm (deleted)
	* lib/Dumper/GFF/GFFV3.pm (modified)
	* lib/Dumper/SpaceBase.pm (deleted)
	* lib/Error/docs (deleted)
	* lib/Fasta.pm (modified)
	* lib/FastaChunker.pm (modified)
	* lib/FastaFile.pm (modified)
	* lib/GFFDB.pm (added)
	* lib/GI.pm (added)
	* lib/Iterator.pm (modified)
	* lib/Iterator/Any.pm (added)
	* lib/Iterator/Fasta.pm (modified)
	* lib/Iterator/GFF3.pm (added)
	* lib/PhatHit.pm (deleted)
	* lib/PhatHit_utils.pm (modified)
	* lib/PhatHsp.pm (deleted)
	* lib/Process/MakerChunk.pm (deleted)
	* lib/Process/MakerTiers.pm (deleted)
	* lib/Process/MpiChunk.pm (added)
	* lib/Process/MpiTiers.pm (added)
	* lib/Shared_Functions.pm (deleted)
	* lib/Widget/.snap.pm.swp (deleted)
	* lib/Widget/RepeatMasker.pm (modified)
	* lib/Widget/augustus.pm (modified)
	* lib/Widget/blastn.pm (modified)
	* lib/Widget/blastx.pm (modified)
	* lib/Widget/exonerate/est2genome.pm (modified)
	* lib/Widget/exonerate/est2genome.pm_orig (deleted)
	* lib/Widget/exonerate/est2genome.pm_rev (deleted)
	* lib/Widget/exonerate/protein2genome.pm (modified)
	* lib/Widget/exonerate/protein2genome.pm_orig (deleted)
	* lib/Widget/exonerate/protein2genome.pm_rev (deleted)
	* lib/Widget/fgenesh.pm (modified)
	* lib/Widget/formatdb.pm (added)
	* lib/Widget/pressdb.pm (added)
	* lib/Widget/setdb.pm (added)
	* lib/Widget/snap.pm (modified)
	* lib/Widget/tblastx.pm (modified)
	* lib/Widget/xdformat.pm (modified)
	* lib/augustus (deleted)
	* lib/clean.pm (modified)
	* lib/cluster.pm (modified)
	* lib/compare.pm (modified)
	* lib/ds_utility.pm (added)
	* lib/evaluator/evaluate.pm (modified)
	* lib/evaluator/funs.pm (modified)
	* lib/evaluator/gff3_to_phatHit (added)
	* lib/evaluator/gff3_to_phatHit/FlyBase.pm (added)
	* lib/evaluator/gff3_to_phatHit/Maker.pm (added)
	* lib/evaluator/gff3_to_phatHit/WormBase.pm (added)
	* lib/evaluator/gff3_to_phatHit/gff3_classifier.pm (added)
	* lib/evaluator/hey_gff3_to_phatHit.pm (added)
	* lib/evaluator/maker_gff.pm (added)
	* lib/evaluator/master_codes (added)
	* lib/evaluator/quality_index.pm (added)
	* lib/evaluator/quality_seq.pm (modified)
	* lib/exonerate/PhatHSP (deleted)
	* lib/exonerate/PhatHit (deleted)
	* lib/exonerate/splice_info.pm (modified)
	* lib/external_gff (added)
	* lib/external_gff/PhatHit.pm (added)
	* lib/external_gff/PhatHsp.pm (added)
	* lib/fgenesh (deleted)
	* lib/maker/auto_annotator.pm (modified)
	* lib/maker/join.pm (modified)
	* lib/maker/quality_index.pm (modified)
	* lib/polisher.pm (modified)
	* lib/polisher/exonerate/est.pm (modified)
	* lib/polisher/exonerate/protein.pm (modified)
	* lib/repeat_mask_seq.pm (modified)
	* lib/repeatmasker (deleted)
	* lib/runlog.pm (modified)
	* lib/snap (deleted)
	major maker update, gff passthrough, evaluator integration, tblastx,
	ncbi, error control

11/26/08 10:50:21 hao [123]
	* bin/maker (modified)


10/21/08 13:55:49 cholt [116]
	* bin/add_utr_gff (added)
	* bin/add_utr_gff.pl (deleted)
	* bin/gff3_merge (added)
	* bin/maker2zff (added)
	* bin/maker2zff.pl (deleted)
	* bin/maker_manager (deleted)
	* bin/split_fasta (added)
	added tools to maker

10/03/08 12:04:06 cholt [111]
	* MPI/mpi_maker (modified)
	* bin/maker (modified)
	* lib/Process/MakerChunk.pm (modified)
	* lib/Process/MakerTiers.pm (modified)
	* lib/Shared_Functions.pm (modified)
	* lib/runlog.pm (modified)
	tblastx mpi_maker

10/02/08 15:00:55 cholt [109]
	* bin/maker (modified)
	* lib/Process/MakerChunk.pm (modified)
	* lib/Process/MakerTiers.pm (modified)
	* lib/Shared_Functions.pm (modified)
	* 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/snap.pm (modified)
	* lib/Widget/tblastx.pm (modified)
	tblastx added to maker

09/26/08 11:26:00 cholt [108]
	* bin/maker (modified)
	* lib/Bio/Search/HSP/PhatHSP/blastp.pm (deleted)
	* lib/Bio/Search/HSP/PhatHSP/tblastn.pm (deleted)
	* lib/Bio/Search/HSP/PhatHSP/tblastx.pm (modified)
	* lib/Bio/Search/Hit/PhatHit/blastp.pm (deleted)
	* lib/Bio/Search/Hit/PhatHit/tblastn.pm (deleted)
	* lib/Bio/Search/Hit/PhatHit/tblastx.pm (modified)
	* lib/PhatHit_utils.pm (modified)
	* lib/Shared_Functions.pm (modified)
	* lib/Widget/TblastN.pm (deleted)
	* lib/Widget/blastp.pm (deleted)
	* lib/Widget/tblastx.pm (modified)
	* lib/runlog.pm (modified)
	tblastx added

09/16/08 15:52:07 cholt [103]
	* bin/maker (modified)
	* lib/Process/MakerChunk.pm (modified)
	count fix

09/15/08 13:35:22 cholt [101]
	* MPI/mpi_maker (modified)
	* bin/maker (modified)
	* lib/Process/MakerChunk.pm (modified)
	* lib/Shared_Functions.pm (modified)
	clean up temp automatically

09/09/08 16:23:20 cholt [99]
	* bin/maker (modified)
	* lib/Process/MakerChunk.pm (modified)
	snap is now optional

08/28/08 12:31:28 cholt [93]
	* bin/maker (modified)
	* lib/Process/MakerChunk.pm (modified)
	* lib/Shared_Functions.pm (modified)
	snap not always called now

08/26/08 17:15:30 cholt [89]
	* Apollo (added)
	* Apollo/fly.tiers (added)
	* Apollo/gff3.tiers (added)
	* INSTALL (added)
	* MPI (added)
	* MPI/MANIFEST (added)
	* MPI/MANIFEST.SKIP (added)
	* MPI/MPIcar.pm (added)
	* MPI/MPIcar.xs (added)
	* MPI/Makefile.PL (added)
	* MPI/contrib (added)
	* MPI/contrib/cpi (added)
	* MPI/contrib/cpi/Makefile (added)
	* MPI/contrib/cpi/cpi.PL (added)
	* MPI/contrib/cpi/cpi.c (added)
	* MPI/contrib/heat (added)
	* MPI/contrib/heat/Makefile (added)
	* MPI/contrib/heat/heat_plate_mpi.PL (added)
	* MPI/contrib/heat/heat_plate_mpi.f (added)
	* MPI/contrib/perf (added)
	* MPI/contrib/perf/Makefile (added)
	* MPI/contrib/perf/mpi_timing.PL (added)
	* MPI/contrib/perf/mpi_timing.c (added)
	* MPI/contrib/perf/runtiming.pl (added)
	* MPI/docs (added)
	* MPI/docs/MPI-C-Bindings.txt (added)
	* MPI/docs/README (added)
	* MPI/docs/TODO (added)
	* MPI/docs/paper.tex (added)
	* MPI/mpi_maker (added)
	* MPI/t (added)
	* MPI/t/00_use_mpi.t (added)
	* MPI/t/01_mpi_init.PL (added)
	* MPI/t/01_mpi_init.t (added)
	* MPI/t/02_mpi_finalize.PL (added)
	* MPI/t/02_mpi_finalize.t (added)
	* MPI/t/03_mpi_comm_rank.PL (added)
	* MPI/t/03_mpi_comm_rank.t (added)
	* MPI/t/04_mpi_comm_size.PL (added)
	* MPI/t/04_mpi_comm_size.t (added)
	* MPI/t/05_mpi_initialized.PL (added)
	* MPI/t/05_mpi_initialized.t (added)
	* MPI/t/06_mpi_sendrecv.PL (added)
	* MPI/t/06_mpi_sendrecv.t (added)
	* MPI/t/06_sendrecv_dbl.PL (added)
	* MPI/t/06_sendrecv_dbl.t (added)
	* MPI/t/06_sendrecv_dblarray.PL (added)
	* MPI/t/06_sendrecv_dblarray.t (added)
	* MPI/t/06_sendrecv_flt.PL (added)
	* MPI/t/06_sendrecv_flt.t (added)
	* MPI/t/06_sendrecv_fltarray.PL (added)
	* MPI/t/06_sendrecv_fltarray.t (added)
	* MPI/t/06_sendrecv_int.PL (added)
	* MPI/t/06_sendrecv_int.t (added)
	* MPI/t/06_sendrecv_intarray.PL (added)
	* MPI/t/06_sendrecv_intarray.t (added)
	* MPI/t/07_mpi_bcast.PL (added)
	* MPI/t/07_mpi_bcast.t (added)
	* MPI/t/07_mpi_bcastarray.PL (added)
	* MPI/t/07_mpi_bcastarray.t (added)
	* MPI/t/08_mpi_reduce.PL (added)
	* MPI/t/08_mpi_reduce.t (added)
	* MPI/t/09_mpi_barrier.PL (added)
	* MPI/t/09_mpi_barrier.t (added)
	* MPI/t/10_mpi_wtime.PL (added)
	* MPI/t/10_mpi_wtime.t (added)
	* MPI/t/11_mpi_scattergather.PL (added)
	* MPI/t/11_mpi_scattergather.t (added)
	* MPI/t/11_mpi_scattergatherarray.PL (added)
	* MPI/t/11_mpi_scattergatherarray.t (added)
	* MPI/t/12_mpi_allreduce.PL (added)
	* MPI/t/12_mpi_allreduce.t (added)
	* MPI/t/13_mpi_sendrecv.PL (added)
	* MPI/t/13_mpi_sendrecv.t (added)
	* MPI/t/greetings.c (added)
	* MPI/t/machinefile (added)
	* MPI/typemap (added)
	* MPI/utils.c (added)
	* README (added)
	* bin (added)
	* bin/add_utr_gff.pl (added)
	* bin/maker (added)
	* bin/maker2zff.pl (added)
	* bin/maker_manager (added)
	* bin/special_apps (added)
	* bin/special_apps/convert-hmm.pl (added)
	* bin/special_apps/exonerate_debugger (added)
	* bin/special_apps/maker_ngasp (added)
	* bin/special_apps/transposon_masker (added)
	* data (added)
	* data/dpp_contig.fasta (added)
	* data/dpp_proteins.fasta (added)
	* data/dpp_transcripts.fasta (added)
	* data/te_proteins.fasta (added)
	* lib (added)
	* lib/Bio (added)
	* lib/Bio/Search (added)
	* lib/Bio/Search/HSP (added)
	* lib/Bio/Search/HSP/PhatHSP (added)
	* lib/Bio/Search/HSP/PhatHSP.pod (added)
	* lib/Bio/Search/HSP/PhatHSP/Base.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/blastn.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/blastp.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/blastx.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/tblastn.pm (added)
	* lib/Bio/Search/HSP/PhatHSP/tblastx.pm (added)
	* lib/Bio/Search/Hit (added)
	* lib/Bio/Search/Hit/PhatHit (added)
	* lib/Bio/Search/Hit/PhatHit.pod (added)
	* lib/Bio/Search/Hit/PhatHit/Base.pm (added)
	* lib/Bio/Search/Hit/PhatHit/blastn.pm (added)
	* lib/Bio/Search/Hit/PhatHit/blastp.pm (added)
	* lib/Bio/Search/Hit/PhatHit/blastx.pm (added)
	* lib/Bio/Search/Hit/PhatHit/tblastn.pm (added)
	* lib/Bio/Search/Hit/PhatHit/tblastx.pm (added)
	* lib/Bio/SearchIO (added)
	* lib/Bio/SearchIO/wublasttable.pm (added)
	* lib/CGL (added)
	* lib/CGL/Annotation (added)
	* lib/CGL/Annotation.pm (added)
	* lib/CGL/Annotation/Feature (added)
	* lib/CGL/Annotation/Feature.pm (added)
	* lib/CGL/Annotation/Feature/Contig.pm (added)
	* lib/CGL/Annotation/Feature/Exon.pm (added)
	* lib/CGL/Annotation/Feature/Gene.pm (added)
	* lib/CGL/Annotation/Feature/Intron.pm (added)
	* lib/CGL/Annotation/Feature/Protein.pm (added)
	* lib/CGL/Annotation/Feature/Sequence_variant.pm (added)
	* lib/CGL/Annotation/Feature/Transcript.pm (added)
	* lib/CGL/Annotation/FeatureLocation.pm (added)
	* lib/CGL/Annotation/FeatureRelationship.pm (added)
	* lib/CGL/Annotation/GFF3 (added)
	* lib/CGL/Annotation/GFF3/DictyBase.pm (added)
	* lib/CGL/Annotation/GFF3/FlyBase.pm (added)
	* lib/CGL/Annotation/GFF3/Maker.pm (added)
	* lib/CGL/Annotation/GFF3/Maker_snap.pm (added)
	* lib/CGL/Annotation/GFF3/WormBase.pm (added)
	* lib/CGL/Annotation/GFF3/nGASP.pm (added)
	* lib/CGL/Annotation/GFF3/nGASP2.pm (added)
	* lib/CGL/Annotation/Iterator.pm (added)
	* lib/CGL/Annotation/Trace.pm (added)
	* lib/CGL/Clone.pm (added)
	* lib/CGL/Ontology (added)
	* lib/CGL/Ontology/GO.pm (added)
	* lib/CGL/Ontology/Node.pm (added)
	* lib/CGL/Ontology/NodeRelationship.pm (added)
	* lib/CGL/Ontology/Ontology.pm (added)
	* lib/CGL/Ontology/Parser (added)
	* lib/CGL/Ontology/Parser/OBO.pm (added)
	* lib/CGL/Ontology/SO.pm (added)
	* lib/CGL/Ontology/Trace.pm (added)
	* lib/CGL/Revcomp.pm (added)
	* lib/CGL/TranslationMachine.pm (added)
	* lib/CGL/Version.pm (added)
	* lib/CGL/gene_ontology.obo (added)
	* lib/CGL/so.new.obo (added)
	* lib/CGL/so.obo (added)
	* lib/CGL/sofa.obo (added)
	* lib/Datastore (added)
	* lib/Datastore/Base.pm (added)
	* lib/Datastore/CG.pm (added)
	* lib/Datastore/MD5.pm (added)
	* lib/Datastore/bin (added)
	* lib/Datastore/bin/ds_dir (added)
	* lib/Datastore/bin/ds_do (added)
	* lib/Datastore/docs (added)
	* lib/Datastore/docs/Datastore::Base.3pm (added)
	* lib/Datastore/docs/Datastore::CG.3pm (added)
	* lib/Datastore/docs/Datastore::MD5.3pm (added)
	* lib/Datastore/docs/ds_dir.1 (added)
	* lib/Datastore/docs/ds_do.1 (added)
	* lib/Dumper (added)
	* lib/Dumper/GFF (added)
	* lib/Dumper/GFF/GFF3.pm (added)
	* lib/Dumper/GFF/GFF3_DEF.pm (added)
	* lib/Dumper/GFF/GFFV3.pm (added)
	* lib/Dumper/SpaceBase.pm (added)
	* lib/Dumper/XML (added)
	* lib/Dumper/XML/Game.pm (added)
	* lib/Dumper/XML/Game_Xml.pm (added)
	* lib/Error (added)
	* lib/Error.pm (added)
	* lib/Error/Simple.pm (added)
	* lib/Error/docs (added)
	* lib/Error/docs/Error.3pm (added)
	* lib/Error/docs/Error::Simple.3pm (added)
	* lib/Fasta.pm (added)
	* lib/FastaChunk.pm (added)
	* lib/FastaChunker.pm (added)
	* lib/FastaFile.pm (added)
	* lib/Iterator (added)
	* lib/Iterator.pm (added)
	* lib/Iterator/Fasta.pm (added)
	* lib/PhatHit.pm (added)
	* lib/PhatHit_utils.pm (added)
	* lib/PhatHsp.pm (added)
	* lib/PostData.pm (added)
	* lib/Process (added)
	* lib/Process/MakerChunk.pm (added)
	* lib/Process/MakerTiers.pm (added)
	* lib/Shadower.pm (added)
	* lib/Shared_Functions.pm (added)
	* lib/SimpleCluster.pm (added)
	* lib/SpaceBase.pm (added)
	* lib/Widget (added)
	* lib/Widget.pm (added)
	* lib/Widget/.snap.pm.swp (added)
	* lib/Widget/PolyBayes.pm (added)
	* lib/Widget/RepeatMasker.pm (added)
	* lib/Widget/TblastN.pm (added)
	* lib/Widget/augustus.pm (added)
	* lib/Widget/blastn.pm (added)
	* lib/Widget/blastp.pm (added)
	* lib/Widget/blastx.pm (added)
	* lib/Widget/exonerate (added)
	* lib/Widget/exonerate.pm (added)
	* lib/Widget/exonerate/est2genome.pm (added)
	* lib/Widget/exonerate/est2genome.pm_orig (added)
	* lib/Widget/exonerate/est2genome.pm_rev (added)
	* lib/Widget/exonerate/protein2genome.pm (added)
	* lib/Widget/exonerate/protein2genome.pm_orig (added)
	* lib/Widget/exonerate/protein2genome.pm_rev (added)
	* lib/Widget/geneid.pm (added)
	* lib/Widget/genscan.pm (added)
	* lib/Widget/primer3.pm (added)
	* lib/Widget/qrna.pm (added)
	* lib/Widget/snap.pm (added)
	* lib/Widget/tblastx.pm (added)
	* lib/Widget/xdformat.pm (added)
	* lib/augustus (added)
	* lib/augustus/PhatHit.pm (added)
	* lib/augustus/PhatHsp.pm (added)
	* lib/auto (added)
	* lib/auto/Datastore (added)
	* lib/auto/Datastore/.packlist (added)
	* lib/auto/Datastore/Base (added)
	* lib/auto/Datastore/Base/autosplit.ix (added)
	* lib/auto/Datastore/CG (added)
	* lib/auto/Datastore/CG/autosplit.ix (added)
	* lib/auto/Datastore/MD5 (added)
	* lib/auto/Datastore/MD5/autosplit.ix (added)
	* lib/auto/Error (added)
	* lib/auto/Error/.packlist (added)
	* lib/clean.pm (added)
	* lib/cluster.pm (added)
	* lib/compare.pm (added)
	* lib/evaluator (added)
	* lib/exonerate (added)
	* lib/exonerate/PhatHSP (added)
	* lib/exonerate/PhatHSP/est2genome.pm (added)
	* lib/exonerate/PhatHSP/protein2genome.pm (added)
	* lib/exonerate/PhatHit (added)
	* lib/exonerate/PhatHit/est2genome.pm (added)
	* lib/exonerate/PhatHit/protein2genome.pm (added)
	* lib/exonerate/splice_info.pm (added)
	* lib/maker (added)
	* lib/maker/auto_annotator.pm (added)
	* lib/maker/join.pm (added)
	* lib/maker/quality_index.pm (added)
	* lib/maker/sens_spec.pm (added)
	* lib/perllocal.pod (added)
	* lib/polisher (added)
	* lib/polisher.pm (added)
	* lib/polisher/exonerate (added)
	* lib/polisher/exonerate.pm (added)
	* lib/polisher/exonerate/est.pm (added)
	* lib/polisher/exonerate/protein.pm (added)
	* lib/repeat_mask_seq.pm (added)
	* lib/repeatmasker (added)
	* lib/repeatmasker/PhatHit.pm (added)
	* lib/repeatmasker/PhatHsp.pm (added)
	* lib/runlog.pm (added)
	* lib/snap (added)
	* lib/snap/PhatHit.pm (added)
	* lib/snap/PhatHsp.pm (added)
	* lib/verifier (added)
	error