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Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 21 20:42:04 2011 UTC (8 years, 9 months ago) by redwards
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_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.11: +6 -2 lines
Diff to previous 1.11
not reopening a file twice!

Revision 1.11 - (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
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00, 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_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_release_2008_09_29
Changes since 1.10: +17 -0 lines
Diff to previous 1.10
Add license words.

Revision 1.10 - (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 1.9: +34 -33 lines
Diff to previous 1.9
*** empty log message ***

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 25 15:29:41 2005 UTC (14 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.8: +1 -1 lines
Diff to previous 1.8
Add compute_contig_md5 as a standalone tool to compute the checksum of a set of contigs.
Fix index_contigs.pl to produce the correct nucleotide counts in the signature file.

Revision 1.8 - (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 1.7: +4 -1 lines
Diff to previous 1.7
addition to gff2seed

Revision 1.7 - (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 1.6: +110 -8 lines
Diff to previous 1.6
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 1.6 - (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 1.5: +366 -72 lines
Diff to previous 1.5
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 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 2 19:36:46 2004 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.4: +3 -1 lines
Diff to previous 1.4
index_contigs should go to organisms directory to get full set

Revision 1.4 - (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
Changes since 1.3: +3 -3 lines
Diff to previous 1.3
cleanup issues relating to large numbers of partial genomes

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 26 04:25:44 2003 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +18 -12 lines
Diff to previous 1.2
defer indexes until after complete load

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Dec 20 15:19:21 2003 UTC (15 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +6 -0 lines
Diff to previous 1.1
for incremental additions to the DB, delete old versions of things

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 20:46:40 2003 UTC (15 years, 11 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-00, V00-00-01, delong-01, delong-02

	get it to work with the release tools

All the rest:
	had to rename foo to foo.pl so that makefiles could recognize
	perl source from, say, Makefiles and READMEs

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