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Revision 1.80 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 15 23:38:32 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, myrast_33, myrast_rel40, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928
Changes since 1.79: +4 -1 lines
Diff to previous 1.79
Protected a "new FIG" in open code with an eval. THIS MUST BE FIXED.

Revision 1.79 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 7 22:18:45 2009 UTC (10 years, 4 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.78: +8 -2 lines
Diff to previous 1.78
Fixed a bug in overlap removal.

Revision 1.78 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 23 03:28:26 2009 UTC (10 years, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.77: +17 -18 lines
Diff to previous 1.77
Switched default to GLIMMER-3; Replaced some backticks; removed a misplaced debug block.

Revision 1.77 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 15 23:50:40 2009 UTC (10 years, 6 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.76: +9 -4 lines
Diff to previous 1.76
Fixed failure to remove overlaps of initial ORF candidates against "special" or other pre-existing PEGs.

Revision 1.76 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 24 13:25:26 2008 UTC (10 years, 11 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26
Changes since 1.75: +268 -68 lines
Diff to previous 1.75
Added GLIMMER-3 support, and enhanced ambig support.

Revision 1.75 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 6 17:55:19 2008 UTC (11 years, 5 months ago) by gdpusch
Branch: MAIN
CVS Tags: mgrast_rel_2008_0625, mgrast_rel_2008_0806, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_2008_0924, rast_rel_2008_07_21, rast_rel_2008_08_07, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_release_2008_09_29
Changes since 1.74: +21 -2 lines
Diff to previous 1.74
Fixed bug in ORF::seq(); minor changes in debugging output. -- /gdp

Revision 1.74 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 14:54:55 2008 UTC (11 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.73: +130 -7 lines
Diff to previous 1.73
Final clean-up. -- /gdp

Revision 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 22 02:03:38 2007 UTC (11 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.72: +7 -2 lines
Diff to previous 1.72
Made sure to close formerly dangling filehandles in &import_features(). -- /gdp

Revision 1.72 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 20 07:51:10 2007 UTC (11 years, 10 months ago) by gdpusch
Branch: MAIN
Changes since 1.71: +4 -4 lines
Diff to previous 1.71
Downgraded invalid STARTs from "FATAL" to "WARNING." -- /gdp

Revision 1.71 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 12 23:32:27 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.70: +1 -1 lines
Diff to previous 1.70
Fixed silly attempt to access a FIG routine via "$self". -- /gdp

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 12 22:19:14 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.69: +150 -112 lines
Diff to previous 1.69
Suppress rejections of possibly truncated PEGs. -- /gdp

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 11 20:47:05 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.68: +18 -16 lines
Diff to previous 1.68
Fixed mind-bogglingly severe error introduced by multiexon hack. -- /gdp

Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 11 15:04:27 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.67: +52 -41 lines
Diff to previous 1.67
Hack attempting to evade warnings from internal STOPs in selenoproteins, pyrrolysoproteins, and frameshift corrections. -- /gdp

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 11 05:17:44 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.66: +2 -1 lines
Diff to previous 1.66
Fixed export error corrupting multi-exon locations. -- /gdp

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 8 23:28:14 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.65: +4 -0 lines
Diff to previous 1.65
Trim off any trailing STOP chars from imported sequences. -- /gdp

Revision 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 8 23:19:05 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.64: +1 -2 lines
Diff to previous 1.64
Minor patch to error-checking on &set_feature_sequence()

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 8 20:24:29 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.63: +13 -13 lines
Diff to previous 1.63
Removed the default computaion of RNAs if not present. -- /gdp

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 7 07:54:27 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.62: +183 -349 lines
Diff to previous 1.62
Removed suppression of multi-exon PEGs. -- /gdp

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 4 23:17:41 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.61: +40 -19 lines
Diff to previous 1.61
Fixed logic error in whether or not RNAs should be recomputed. -- /gdp

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 3 20:11:58 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.60: +3 -1 lines
Diff to previous 1.60
Added option to suppress import. -- /gdp

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 30 23:32:54 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.59: +1 -1 lines
Diff to previous 1.59
Fixed debugging statement that may be causing excessively large logfiles. -- /gdp

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 30 21:30:55 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.58: +19 -1 lines
Diff to previous 1.58
Fixed bug in &to_seed_loc(). -- /gdp

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 18 16:08:53 2007 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.57: +4 -2 lines
Diff to previous 1.57
Switch to using new Niels RNA finder; still allow override via
RP_SEARCH_FOR_RNAS envar.

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 17 18:00:47 2007 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.56: +11 -4 lines
Diff to previous 1.56
some more error checking

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 16 18:32:29 2007 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.55: +7 -1 lines
Diff to previous 1.55
If an envar RP_SEARCH_FOR_RNAS exists, use that for RNA finding. It will be invoked

toolname --contigs=$dir/contigs --orgid=$taxid --domain=$domain --genus=$genus --species=$species --log=$dir/rna.log

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 31 16:45:50 2007 UTC (12 years, 3 months ago) by gdpusch
Branch: MAIN
Changes since 1.54: +78 -36 lines
Diff to previous 1.54
Temporary hacks so that attenpts to import multi-exon and selenocysteine PEGs are just ignored, not fatal. -- /gdp

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 29 13:59:44 2007 UTC (12 years, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.53: +2 -3 lines
Diff to previous 1.53
Added support for kmer statistics. -- /gdp

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 29 13:51:18 2007 UTC (12 years, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.52: +39 -36 lines
Diff to previous 1.52
Added support for kmer statistics. -- /gdp

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 29 13:27:39 2007 UTC (12 years, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.51: +166 -0 lines
Diff to previous 1.51
Added support for kmer statistics. -- /gdp

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 1 16:01:13 2007 UTC (12 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.50: +4 -0 lines
Diff to previous 1.50
Rollup of changes for the new RAST install.

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 17 13:47:28 2007 UTC (12 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.49: +48 -47 lines
Diff to previous 1.49
Restructured "&export_features()" to (hopefully) eliminate NFS errors. -- /gdp

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 17 12:48:06 2007 UTC (12 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.48: +69 -27 lines
Diff to previous 1.48
Fixed errors in alternate genetic code support; added debugging statements. -- /gdp

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 11 04:17:07 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.47: +6 -4 lines
Diff to previous 1.47
Fixed stupid error in handling alternate genetic codes. -- /gdp

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 9 16:52:11 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.46: +23 -6 lines
Diff to previous 1.46
Added support for alternate genetic codes. -- /gdp

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 27 19:14:35 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.45: +2 -2 lines
Diff to previous 1.45
fixes to rapid propagation

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 11 04:26:49 2007 UTC (12 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.44: +13 -0 lines
Diff to previous 1.44
Added check against duplicate contig IDs. -- /gdp

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 15:19:19 2006 UTC (12 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.43: +28 -7 lines
Diff to previous 1.43
Rollup commit of 48hr changes.

Added add_virtual_genome to Subsystem.pm to support UnvSubsys doing
the right thing when handed a FIGV.

Added propagation of 48hr_job thru the various link generation scripts in order for protein.cgi/display_subsys.cgi
to properly show virtual genomes.

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 15 19:10:40 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.42: +2 -1 lines
Diff to previous 1.42
fixes for 48hr server

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 28 14:23:55 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.41: +6 -4 lines
Diff to previous 1.41
Minor cosmetic changes. -- /gdp

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 14 03:58:00 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.40: +7 -7 lines
Diff to previous 1.40
Fixed Yet Another Bug in &call_starts(). Increase threshold for verbosity in &search_(up|down)stream_for_(start|stop)(). -- /gdp

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 13 21:32:33 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.39: +1 -1 lines
Diff to previous 1.39
Fixed failure to initialize $tmp_loc in &add_feature() to support new definition of ORF object translations. -- /gdp

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 13 21:24:23 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.38: +1 -4 lines
Diff to previous 1.38
Fixed failure to initialize $tmp_loc in &add_feature() to support new definition of ORF object translations. -- /gdp

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 13 21:14:34 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.37: +51 -40 lines
Diff to previous 1.37
Modified &possible_orfs() and &recall_orfs() to preserve length of GLIMMER call. -- /gdp

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 13 20:07:36 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.36: +6 -9 lines
Diff to previous 1.36
Raised threshold verbosity on inner loop of &possible_starts(). -- /gdp

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 13 18:40:24 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.35: +25 -6 lines
Diff to previous 1.35
Added G+C content; set score to zero below 7% iden; truncated sim voting to top 10. -- /gdp

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 13 14:56:44 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.34: +1 -1 lines
Diff to previous 1.34
Fixed error in length estimate. -- /gdp

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 12 06:41:09 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.33: +28 -101 lines
Diff to previous 1.33
Re-wrote &call_starts(). -- /gdp

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 10 19:17:19 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.32: +3 -2 lines
Diff to previous 1.32
Fixed logic to import all features by default. -- /gdp

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 10 16:11:19 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.31: +8 -4 lines
Diff to previous 1.31
Fixed and added debugging info. -- /gdp

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 9 04:15:46 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.30: +133 -92 lines
Diff to previous 1.30
Fixed problems with ORF initialization. -- /gdp

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 5 20:52:22 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.29: +5 -5 lines
Diff to previous 1.29
More fixed to caching START and STOP seraches. -- /gdp

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 5 17:58:12 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.28: +107 -48 lines
Diff to previous 1.28
Auto-memoization introduced a bug; now caching manually. -- /gdp

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 5 03:05:31 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.27: +7 -7 lines
Diff to previous 1.27
Fixed typos and duplicated subroutine names. -- /gdp

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 5 02:13:56 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.26: +5 -3 lines
Diff to previous 1.26
Fixed error-msg I forgot to complete. -- /gdp

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 5 00:26:22 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.25: +550 -257 lines
Diff to previous 1.25
Major re-write of &call_starts(). &get_contig_seq() changed to &get_contig_seqP(); now returns a pointer, rather than the contig sequence. Mow caching contig lens in memory, rather than re-computing them each time. Memoized &search_for_(up|down)stream_(start|stop)() to save CPU time. -- /gdp

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 22 05:38:45 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.24: +107 -55 lines
Diff to previous 1.24
Fixed bugs in ORF-promotion subroutine. -- /gdp

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 18 02:19:34 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.23: +6 -4 lines
Diff to previous 1.23
promote remaining orfs in rapid_propagation

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 18 00:26:39 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.22: +31 -3 lines
Diff to previous 1.22
initial undebugged rapid propagation script

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 15 11:25:42 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.21: +9 -0 lines
Diff to previous 1.21
fix yet another bug in all_bbhs - this one relating to deleted_fids

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 14 22:59:36 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.20: +7 -4 lines
Diff to previous 1.20
Improved VERBOSE reporting within orf-promotion routines. -- /gdp

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 13 14:43:40 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.19: +30 -10 lines
Diff to previous 1.19
Hack-fixes of various import problems (split PEGs, etc.), not properly done. -- /gdp

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 13 02:35:44 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +349 -17 lines
Diff to previous 1.18
Added peg-promotion and overlap removal. -- /gdp

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 7 05:29:07 2006 UTC (13 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.17: +18 -0 lines
Diff to previous 1.17
Added test for used ORfs. -- /gdp

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 11 10:56:42 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +33 -12 lines
Diff to previous 1.16
Fixed error in &import_features(all). Added various diagnostics. -- /gdp

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 29 18:07:44 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.15: +7 -7 lines
Diff to previous 1.15
set up find_neighbors to handle existing genomes

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 29 00:04:50 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.14: +155 -42 lines
Diff to previous 1.14
Fixed numerous bugs. -- /gdp

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 27 22:48:31 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.13: +42 -30 lines
Diff to previous 1.13
Fixed major bug in &call_starts(). -- /gdp

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 25 14:30:42 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +38 -20 lines
Diff to previous 1.12
Fixed numerous bugs, and added several features. -- /gdp

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 24 23:22:30 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +691 -283 lines
Diff to previous 1.11
Added missing ORF-object wrapper for call_start(). -- /gdp

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 7 04:03:10 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +2 -2 lines
Diff to previous 1.10
add new_versions_of_features

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 26 21:57:23 2006 UTC (13 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +156 -19 lines
Diff to previous 1.9
fix building FigFamData

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 19 13:23:02 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +10 -1 lines
Diff to previous 1.8
fix find_neighbors to allow for new family IDs

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 14 02:47:22 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +104 -59 lines
Diff to previous 1.7
Added various features, including structures to support overlap detection and removal. -- /gdp

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 12 13:10:38 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +397 -70 lines
Diff to previous 1.6
fixes to making assignments based on consistency

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 5 00:17:04 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +103 -18 lines
Diff to previous 1.5
Fixed PEG, ORF sequence STOP-codon bug; added link to RNA-finding code. -- /gdp

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 3 19:28:52 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +56 -12 lines
Diff to previous 1.4
updates to ARPP/STAG

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 1 18:24:23 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +119 -46 lines
Diff to previous 1.3
fixes and errors to STAG

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 31 20:31:19 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +3 -3 lines
Diff to previous 1.2
Appended $ENV{VERBOSE} to some debugging statements. -- /gdp

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 31 19:37:40 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +102 -47 lines
Diff to previous 1.1
next version of the STAG code

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 25 23:12:56 2006 UTC (13 years, 7 months ago) by overbeek
Branch: MAIN
add very buggy start of NewGenome.pm and FigFam stuff

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