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Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 25 19:54:01 2012 UTC (7 years, 5 months ago) by gdpusch
Branch: MAIN
CVS Tags: HEAD, mgrast_version_3_2, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.25: +3 -1 lines
Diff to previous 1.25
Grandfather in "-just_mark" in addition to "-justMark".

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 17 08:57:48 2011 UTC (8 years, 10 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, myrast_33, myrast_rel40, rast_rel_2011_0119, rast_rel_2011_0928
Changes since 1.24: +32 -7 lines
Diff to previous 1.24
Replaced dies with warn and exit if '-nofatal', so that script fails gracefully if no neighbors exist.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 25 17:57:26 2010 UTC (8 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.23: +7 -5 lines
Diff to previous 1.23
loosened constraints

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 22 22:58:17 2010 UTC (9 years ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.22: +1 -0 lines
Diff to previous 1.22
Fixed failure to log PEG being corrected.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 20 18:38:42 2010 UTC (9 years, 2 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_0928
Changes since 1.21: +9 -6 lines
Diff to previous 1.21
Fixed coordinate mapping used in BLAST hit extension.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 28 15:56:34 2010 UTC (9 years, 3 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.20: +134 -129 lines
Diff to previous 1.20
Modified to use Kmers.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 28 06:02:33 2010 UTC (9 years, 5 months ago) by gdpusch
Branch: MAIN
Changes since 1.19: +7 -2 lines
Diff to previous 1.19
Modfied to use either "closest.genomes" or "neighbors"

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 4 20:33:44 2009 UTC (10 years ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.18: +37 -1 lines
Diff to previous 1.18
add a line describing template

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 22 12:14:01 2009 UTC (10 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.17: +14 -5 lines
Diff to previous 1.17
support just marking frameshifts

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 27 21:09:42 2009 UTC (10 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2009_07_09, rast_rel_2009_0925
Changes since 1.16: +4 -5 lines
Diff to previous 1.16
fix fencepost error occurring with input with 3 or 4 neighbors. pushed to production rast as a patch.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 15 23:42:07 2009 UTC (10 years, 6 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.15: +61 -55 lines
Diff to previous 1.15
Supress FS correction if a PEG is in "special_pegs" file, to prevent incorrect deletion of seleocysteine and pyrrolysine codons from selenoprotein and pyrrolysoprotein PEGs.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 20 15:34:01 2009 UTC (10 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.14: +27 -3 lines
Diff to previous 1.14
Make the neighbor parsing more verbose in the case of errors.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 1 14:10:53 2008 UTC (11 years, 1 month ago) by gdpusch
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, 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
Changes since 1.13: +10 -3 lines
Diff to previous 1.13
Fixed divide-by-zero problem in sims loop, and added explicit test of id1 sequence length. -- /gdp

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 22 19:33:09 2008 UTC (11 years, 6 months ago) by overbeek
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, rast_2008_0924, 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_release_2008_09_29
Changes since 1.12: +2 -9 lines
Diff to previous 1.12
shift position of correct_frameshifts in rapid_propagation pipeline

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 21 18:05:54 2008 UTC (11 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.11: +1 -0 lines
Diff to previous 1.11
delete tbl entries for fids making up a frameshift

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 13 14:54:27 2008 UTC (11 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.10: +5 -4 lines
Diff to previous 1.10
Final clean-up. -- /gdp

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 9 02:17:48 2008 UTC (11 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.9: +9 -0 lines
Diff to previous 1.9
correct_frameshifts now records new calls in called_by and records those in FIGfams in the found file

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jan 31 15:31:39 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.8: +0 -2 lines
Diff to previous 1.8
Put reporting of family directory used in the FigFams constructor, only printed if REPORT_FIGFAM_DETAILS
is specified in the environment.

Make the FIG_Config defaulting work properly for the figfams directory.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 30 22:50:37 2008 UTC (11 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.7: +2 -0 lines
Diff to previous 1.7
Log the pathname to the figfams directory used for the analysis.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 16 03:59:26 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +1 -1 lines
Diff to previous 1.6
turn off a debugging message in correct_frameshifts.pl

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 16 03:56:10 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5
fixes to frameshift correction

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 8 21:21:23 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +9 -1 lines
Diff to previous 1.4
fixes to correct_frameshifts.pl to get locations right

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 4 12:34:49 2007 UTC (11 years, 11 months ago) by gdpusch
Branch: MAIN
Changes since 1.3: +2 -2 lines
Diff to previous 1.3
Fixed missing "$figV" argument to FigFams->new(). -- /gdp

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 3 14:56:06 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +1 -1 lines
Diff to previous 1.2
add assignments to annotations in correct_frameshifts.pl

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 3 13:08:49 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +20 -7 lines
Diff to previous 1.1
use FIGfams to assign function for corrected frameshifts

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 3 02:48:25 2007 UTC (11 years, 11 months ago) by overbeek
Branch: MAIN
put in correct_frameshifts

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