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Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 10 12:20:46 2019 UTC (4 weeks, 5 days ago) by gdpusch
Branch: MAIN
CVS Tags: HEAD
Changes since 1.26: +178 -160 lines
Diff to previous 1.26
Major rewrite, processing sequences using 'gjoseqlib' and arguments using 'Getopt::Long::Descriptive'.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 24 22:41:13 2017 UTC (2 years, 8 months ago) by gdpusch
Branch: MAIN
Changes since 1.25: +1 -1 lines
Diff to previous 1.25
Fixed missing argument-type for --logfile argument

Revision 1.25 - (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
Changes since 1.24: +288 -239 lines
Diff to previous 1.24
Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that PRODIGAL will not bail out.FigKernelPackages/Prodigal.pm

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 12 17:03:06 2010 UTC (8 years, 11 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_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.23: +1 -2 lines
Diff to previous 1.23
Fixed contig-ID "0" bug

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Sep 18 14:33:57 2010 UTC (9 years, 1 month ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.22: +2 -2 lines
Diff to previous 1.22
fix bug that appears with a contig id of "0"

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 27 19:35:08 2010 UTC (9 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.21: +3 -3 lines
Diff to previous 1.21
fix filename/space problem

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 6 16:27:11 2009 UTC (10 years ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2010_0118, rast_rel_2010_0526
Changes since 1.20: +4 -2 lines
Diff to previous 1.20
Added hack to split on very long homopolymer regions.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 28 12:43:03 2009 UTC (10 years, 9 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925
Changes since 1.19: +29 -18 lines
Diff to previous 1.19
Further improved reporting of missing header and zero-length records.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 28 12:05:12 2009 UTC (10 years, 9 months ago) by gdpusch
Branch: MAIN
Changes since 1.18: +10 -4 lines
Diff to previous 1.18
Improved reporting of missing header and zero-length records, and suppressed a stray debugging statement.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 4 21:52:34 2008 UTC (10 years, 11 months ago) by gdpusch
Branch: MAIN
CVS Tags: rast_rel_2008_12_18
Changes since 1.17: +12 -2 lines
Diff to previous 1.17
Hack to fix problem with contig-IDs ending with commas.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 6 19:34:26 2008 UTC (11 years ago) by gdpusch
Branch: MAIN
CVS Tags: mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, rast_rel_2008_11_24
Changes since 1.16: +32 -20 lines
Diff to previous 1.16
Additional support for runs of ambigs

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 11 21:47:00 2008 UTC (11 years, 3 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, rast_2008_0924, 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_release_2008_09_29
Changes since 1.15: +2 -2 lines
Diff to previous 1.15
Modified to split on runs of ambigs, not just N or X. -- /gdp

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 11 21:42:03 2008 UTC (11 years, 3 months ago) by gdpusch
Branch: MAIN
Changes since 1.14: +20 -12 lines
Diff to previous 1.14
Modified to split on runs of ambigs, not just N or X. -- /gdp

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 12 22:30:51 2008 UTC (11 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_07_21
Changes since 1.13: +13 -1 lines
Diff to previous 1.13
add max id fix, infinte loop fix.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 7 22:05:13 2008 UTC (11 years, 6 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_06_16, rast_rel_2008_06_18
Changes since 1.12: +105 -53 lines
Diff to previous 1.12
Clean up for use strict.
Add options:
	-renumber-digits to set the number of digits in the renumbered contig names
	-renumber-prefix to set the prefix for the new names
	-renumber-map to keep track of the renumbered names
	-remove-duplicates to remove duplicate contigs
	-duplicates-file to remember the duplicates

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 12 21:20:01 2007 UTC (12 years, 1 month ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2008_04_23
Changes since 1.11: +17 -0 lines
Diff to previous 1.11
add bad-error limit so we don't spam our error logs.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 12 21:09:34 2007 UTC (12 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.10: +6 -6 lines
Diff to previous 1.10
accept ASCII.*text in file(1) output.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Sep 16 20:18:15 2007 UTC (12 years, 1 month ago) by gdpusch
Branch: MAIN
Changes since 1.9: +41 -2 lines
Diff to previous 1.9
Added file-type check; fixed handling of alternate line-terminators. -- /gdp

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 14 02:48:58 2007 UTC (12 years, 2 months ago) by gdpusch
Branch: MAIN
Changes since 1.8: +10 -7 lines
Diff to previous 1.8
Fixed problem handling leadin whitespace lines. -- /gdp

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 4 00:17:25 2007 UTC (12 years, 5 months ago) by gdpusch
Branch: MAIN
Changes since 1.7: +83 -85 lines
Diff to previous 1.7
Added FASTA validation. -- /gdp

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 1 20:01:49 2007 UTC (12 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.6: +4 -4 lines
Diff to previous 1.6
latest 48hr changes, plus timelogic support in process_new_sims

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 20:04:26 2006 UTC (12 years, 11 months ago) by paczian
Branch: MAIN
Changes since 1.5: +1 -1 lines
Diff to previous 1.5
fixed a missing comma

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 29 19:48:06 2006 UTC (12 years, 11 months ago) by paczian
Branch: MAIN
Changes since 1.4: +22 -10 lines
Diff to previous 1.4
added the logfile option which writes error messages to a logfile instead of STDERR

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 22 12:05:50 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.3: +0 -2 lines
Diff to previous 1.3
Removed stray debugging statement. -- /gdp

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 21 21:49:49 2006 UTC (12 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +73 -32 lines
Diff to previous 1.2
Added explicit file args; suppress scaffold-map when used as a filter. -- /gdp

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 18:56:38 2005 UTC (13 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.1: +17 -0 lines
Diff to previous 1.1
Add license words.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 28 21:43:24 2005 UTC (14 years, 1 month ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00, caBIG-dataload-0
Script to standardize FASTA format contig files; also splits scaffolds into contigs, and filters contigs using length cutoffs. -- /gdp

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