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Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Sun May 10 19:12:31 2009 UTC (10 years, 6 months ago) by olson
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_2009_05_18, rast_rel_2009_07_09, 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, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.24: +3 -2 lines
Diff to previous 1.24
Fix bug where compute_genome_counts fails to run on a genome directory with multiple contigs* files where none is named contigs.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 23 16:14:49 2009 UTC (10 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.23: +3 -1 lines
Diff to previous 1.23
Override "maindomain" as "Plasmid" if /plasmid/ occurs _anywhere, not just at the begining of the TAXONOMY string.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 23 16:10:21 2009 UTC (10 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.22: +2 -2 lines
Diff to previous 1.22
Classify genome as "Plasmid" if /plasmid/ occurs _anywhere, not just at the begining of the TAXONOMY string.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 23 04:18:37 2009 UTC (10 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.21: +1 -1 lines
Diff to previous 1.21
Resolved conflicts between my changes and the last checked-in changes.

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 23 04:10:20 2009 UTC (10 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.20: +60 -28 lines
Diff to previous 1.20
Resolved conflicts between my changes and the last checked-in changes.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Apr 18 15:12:40 2009 UTC (10 years, 6 months ago) by gdpusch
Branch: MAIN
Changes since 1.19: +74 -75 lines
Diff to previous 1.19
Added check to make sure COUNTS exists and is up to date.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 9 18:18:03 2009 UTC (10 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_03_26
Changes since 1.18: +13 -13 lines
Diff to previous 1.18
Slight tweak of fix to TAXONOMY whitespace and "Candidatus" bugs

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 9 17:48:21 2009 UTC (10 years, 9 months ago) by gdpusch
Branch: MAIN
Changes since 1.17: +8 -6 lines
Diff to previous 1.17
Slight tweak of fix to TAXONOMY whitespace and "Candidatus" bugs

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 26 21:10:11 2009 UTC (10 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_02_05
Changes since 1.16: +19 -12 lines
Diff to previous 1.16
Fixed (hopefully) a TAXONOMY-sorting bug, and remaining instances of "Candidatus."

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 28 03:29:18 2006 UTC (12 years, 10 months ago) by golsen
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_release_2008_09_29
Changes since 1.15: +1 -1 lines
Diff to previous 1.15
Fix bug introduced in trying to trim "root" from taxonomies.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 28 02:14:25 2006 UTC (12 years, 10 months ago) by golsen
Branch: MAIN
Changes since 1.14: +14 -6 lines
Diff to previous 1.14
Add support for plasmids as "maindomain" in genome record.
Cover the case of an undefined taxonomy.
(previously copied that of previous genome!)

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 23 19:20:54 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.13: +2 -0 lines
Diff to previous 1.13
changes to support dynamic sims and updates

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 18:56:37 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.12: +17 -0 lines
Diff to previous 1.12
Add license words.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 05:51:06 2005 UTC (14 years, 5 months ago) by parrello
Branch: MAIN
CVS Tags: Root-bobdev_news, caBIG-00-00-00, caBIG-dataload-0, merge-bobdev_news-1, merge-bobdev_news-2, merge-bodev_news-3, merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Branch point for: Branch-bobdev_news
Changes since 1.11: +62 -136 lines
Diff to previous 1.11
*** empty log message ***

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Apr 10 00:15:17 2005 UTC (14 years, 7 months ago) by redwards
Branch: MAIN
CVS Tags: efrank-preMakefileToStandardMk
Changes since 1.10: +2 -1 lines
Diff to previous 1.10
addition to gff2seed

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 8 21:06:04 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.9: +47 -0 lines
Diff to previous 1.9
Add support for computing MD5 checksums for contigs and genomes.

The checksum of a genome is defined as the checksum of its signature file. The signature
file consists of tab-separated lines, one for each contig, ordered by the contig id.
Each line contains the contig ID, the length of the contig in nucleotides, and the
MD5 checksum of the nucleotide data, with uppercase letters forced to lower case.

The signature file is written by index_contigs to
The genome's md5 checksum is written by index_contigs to <genomedir>/MD5SUM.

The md5.c code here is extracted from the Perl Digest::MD5 module. We use the perl
configuration to build it so that it will work correctly on 64-bit architectures.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 27 15:04:39 2004 UTC (15 years ago) by olson
Branch: MAIN
Changes since 1.8: +1 -1 lines
Diff to previous 1.8
mysql doesnt like varchar length > 255

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 24 22:11:50 2004 UTC (15 years, 2 months ago) by olson
Branch: MAIN
Changes since 1.7: +93 -76 lines
Diff to previous 1.7
Gary Olsen's optimized database loading code.

This probably needs to be tweaked to use the full path (FIG_Config::bin/<app>), but I
want to get this committed today.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 25 12:31:22 2004 UTC (15 years, 4 months ago) by overbeek
Branch: MAIN
Changes since 1.6: +2 -2 lines
Diff to previous 1.6
allow leading and trailing blanks on TAXONOMY

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 21 20:03:02 2004 UTC (15 years, 4 months ago) by gdpusch
Branch: MAIN
Changes since 1.5: +6 -5 lines
Diff to previous 1.5
Added count for "Environmental Scales"

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 16 02:58:52 2004 UTC (15 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +18 -3 lines
Diff to previous 1.4
set VERSIONS in genomes

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 6 18:14:48 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +5 -1 lines
Diff to previous 1.3
fix stick behavior for checked sims

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 5 12:26:58 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +30 -13 lines
Diff to previous 1.2
minor bugs

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 29 02:22:37 2003 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +9 -8 lines
Diff to previous 1.1
numerous performance issues

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 28 17:11:29 2003 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
cleanup issues relating to large numbers of partial genomes

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