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Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 24 15:54:16 2015 UTC (3 years, 10 months ago) by gdpusch
Branch: MAIN
CVS Tags: HEAD
Changes since 1.21: +2 -2 lines
Diff to previous 1.21
Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that PRODIGAL will not bail out.FigKernelPackages/Prodigal.pm

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 16 15:02:48 2010 UTC (9 years, 4 months ago) by gdpusch
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, mgrast_version_3_2, myrast_33, myrast_rel40, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.20: +138 -111 lines
Diff to previous 1.20
Fixed major bug handling negative strand; also minor cosmetic changes for readability.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jan 20 21:50:10 2008 UTC (11 years, 10 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_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18, 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_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_release_2008_09_29
Changes since 1.19: +21 -5 lines
Diff to previous 1.19
No longer complains about split loci. -- /gdp

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 30 23:04:16 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.18: +4 -2 lines
Diff to previous 1.18
put in the fr2go stuff

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 15 20:25:47 2006 UTC (13 years ago) by olson
Branch: MAIN
Changes since 1.17: +1 -1 lines
Diff to previous 1.17
fix -h error

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 13 20:19:27 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.16: +1 -1 lines
Diff to previous 1.16
Fixed missing paren introduced by the RNA-overlapping-RNA bug fix. :-( -- /gdp

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 13 19:41:51 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.15: +2 -4 lines
Diff to previous 1.15
Fixed RNA-overlaping-RNA bug. -- /gdp

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 3 18:01:13 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.14: +2 -2 lines
Diff to previous 1.14
Reluctantly modified to allow ambiguity characters in certain START and STOP codon positions, since GLIMMER seems to produce them... :-(  -- /gdp

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 1 17:21:51 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.13: +17 -0 lines
Diff to previous 1.13
Moved `assess_genome_quality.pl` to `assess_gene_call_quality.pl`. -- /gdp

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 29 22:03:05 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.12: +57 -36 lines
Diff to previous 1.12
Fixed severe bug in modified &load_tbl() routine. -- /gdp

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 27 14:48:59 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.11: +9 -2 lines
Diff to previous 1.11
Added check for replaced features. Increased possible-truncation margin, added truncation-flag output. -- /gdp

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 27 13:39:16 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.10: +18 -11 lines
Diff to previous 1.10
allow spaces in abbr for roles in subsystems - fix pattern

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 26 01:04:13 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.9: +37 -15 lines
Diff to previous 1.9
Fixed bug in sma-estrand overlap logic. -- /gdp

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 25 18:47:40 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.8: +20 -25 lines
Diff to previous 1.8
Fixed bug handling truncated PEGs. modified output format to improve parsibility. -- /gdp

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 22 05:39:30 2006 UTC (13 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.7: +11 -8 lines
Diff to previous 1.7
Fixed threshold logic. -- /gdp

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 20 16:10:22 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +2 -2 lines
Diff to previous 1.6
Modified default thresholds. -- /gdp

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 14 22:57:45 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +19 -2 lines
Diff to previous 1.5
Allow OrgDir as a valid input. -- /gdp

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 25 17:45:58 2006 UTC (13 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +9 -8 lines
Diff to previous 1.4
Included overlap thresholds in report. -- /gdp

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 2 17:54:00 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +20 -8 lines
Diff to previous 1.3
Added '-parms' switch and some bulletproofing. -- /gdp

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 2 11:51:06 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +31 -12 lines
Diff to previous 1.2
Added test for RNA overlaps. -- /gdp

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 2 10:47:51 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +26 -6 lines
Diff to previous 1.1
Added test for short features. -- /gdp

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 1 22:16:16 2006 UTC (13 years, 5 months ago) by overbeek
Branch: MAIN
Initial checkin. -- /gdp

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