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Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 28 15:58:09 2010 UTC (9 years, 3 months ago) by gdpusch
Branch: MAIN
CVS Tags: HEAD, 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 1.18: +80 -68 lines
Diff to previous 1.18
Modified to use Kmers.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 15 23:36:00 2009 UTC (10 years, 6 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.17: +45 -9 lines
Diff to previous 1.17
Added hooks for priority-based PEG removal; however, code does not yet appear to be complete. (Still runs, though...)

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 11 04:21:03 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_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_release_2008_09_29
Changes since 1.16: +1 -0 lines
Diff to previous 1.16
Added setting of VERBOSE from metafile. -- /gdp

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 11 04:14:40 2008 UTC (11 years, 5 months ago) by gdpusch
Branch: MAIN
Changes since 1.15: +27 -6 lines
Diff to previous 1.15
Fixed bug in removal logic, and handled case where two PEGs have identical loci. -- /gdp

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 10 03:05:59 2008 UTC (11 years, 5 months ago) by gdpusch
Branch: MAIN
Changes since 1.14: +99 -41 lines
Diff to previous 1.14
Added Ross\'s proposed rules for breaking deadlocks between two frameshifted PEGs. -- /gdp

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 1 17:47:05 2008 UTC (11 years, 5 months ago) by gdpusch
Branch: MAIN
Changes since 1.13: +1 -1 lines
Diff to previous 1.13
Forced removal of OOP call to FIG::display_id_and_seq\(\), due to Bruce's latest un-announced change to FIG.pm, under bitter and strenuous protest. -- /gdp

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 22 03:56:51 2008 UTC (11 years, 5 months ago) by gdpusch
Branch: MAIN
Changes since 1.12: +6 -4 lines
Diff to previous 1.12
Fixed omissions in FIGfam caching and processing frameshifts. -- /gdp

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 9 16:51:45 2008 UTC (11 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.11: +120 -46 lines
Diff to previous 1.11
Added lazy FIGfam placement if PEG is not found in "found" file; reorganized code and added comments. -- /gdp

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 10 20:15:25 2007 UTC (12 years, 1 month ago) by gdpusch
Branch: MAIN
Changes since 1.10: +4 -15 lines
Diff to previous 1.10
Added proper handling of split loci. -- /gdp

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 25 22:40:16 2007 UTC (12 years, 5 months ago) by gdpusch
Branch: MAIN
Changes since 1.9: +31 -10 lines
Diff to previous 1.9
Added support for alternate genetic codes. -- /gdp

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 14 20:00:36 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.8: +42 -15 lines
Diff to previous 1.8
Added metafile support. -- /gdp

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 4 23:14:09 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +27 -24 lines
Diff to previous 1.7
Fixed serious sorting bug introduced by spurious "my". -- /gdp

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 4 21:15:37 2006 UTC (12 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.6: +4 -4 lines
Diff to previous 1.6
48-hr updates.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 4 20:50:44 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +83 -64 lines
Diff to previous 1.5
First attempt at deadlock removal. -- /gdp

Revision 1.5 - (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 1.4: +20 -1 lines
Diff to previous 1.4
put in the fr2go stuff

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 6 20:06:02 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.3: +72 -16 lines
Diff to previous 1.3
Modified to keep PEGs in FIGfams. -- /gdp

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 3 17:59:13 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.2: +24 -13 lines
Diff to previous 1.2
Removed several stupid bugs. -- /gdp

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 23 17:08:58 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Changes since 1.1: +5 -1 lines
Diff to previous 1.1
Added code to overwrite tbl, recompute fasta

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 23 15:00:56 2006 UTC (13 years ago) by overbeek
Branch: MAIN
Script to filter out embedded pegs. -- /gdp

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