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Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 7 18:24:01 2016 UTC (3 years, 9 months ago) by olson
Branch: MAIN
CVS Tags: HEAD
Changes since 1.41: +7 -2 lines
Diff to previous 1.41
Remove duplicated FIG object creation.

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 5 15:32:18 2015 UTC (4 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.40: +7 -2 lines
Diff to previous 1.40
Go back to pulling stats from given sequences.

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 14 17:12:21 2014 UTC (5 years, 8 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2014_0729, rast_rel_2014_0912
Changes since 1.39: +1102 -0 lines
Diff to previous 1.39
add neighbor computation code.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 26 19:47:28 2014 UTC (6 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.38: +4 -4 lines
Diff to previous 1.38
use SeedUtils routines instead of FIG.

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 25 22:35:51 2014 UTC (6 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.37: +133 -1 lines
Diff to previous 1.37
Use SEedUtils translate

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 17 19:32:30 2013 UTC (6 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.36: +6 -3 lines
Diff to previous 1.36
Make work without FIG.pm

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 23 20:58:40 2013 UTC (6 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.35: +2 -0 lines
Diff to previous 1.35
Add SAS declarations.

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 18 13:56:19 2012 UTC (7 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +9 -70 lines
Diff to previous 1.34
better order constraint

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 17 02:08:51 2012 UTC (7 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.33: +3 -2 lines
Diff to previous 1.33
replacing most abundant genus with last common ancestor

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 8 16:24:59 2012 UTC (7 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.32: +37 -10 lines
Diff to previous 1.32
Add support for passing -detailed through to dna kmers.
Add support for retrieving all family calls for protein kmers.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 10 19:10:31 2012 UTC (7 years, 10 months ago) by redwards
Branch: MAIN
CVS Tags: mgrast_version_3_2
Changes since 1.31: +28 -5 lines
Diff to previous 1.31
adding details to the assign to DNA for kmer calls

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 6 17:13:28 2011 UTC (8 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_12152011, mgrast_release_3_1_2
Changes since 1.30: +14 -6 lines
Diff to previous 1.30
Turn some fatal errors into empty returns.
Fix figfam counts to take into account the -1/undef distinction on data returned
from low-level kmer lookups.

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 21:13:24 2011 UTC (8 years, 5 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_10262011
Changes since 1.29: +5 -2 lines
Diff to previous 1.29
fix empty-blast-output bug

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 27 21:56:46 2011 UTC (8 years, 6 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2011_0928
Changes since 1.28: +132 -13 lines
Diff to previous 1.28
Annotation server updates (replace inline code with KmerMgr).
Add tests.

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 10 00:07:27 2010 UTC (9 years, 3 months ago) by olson
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_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, myrast_33, myrast_rel40, rast_rel_2011_0119
Changes since 1.27: +1 -1 lines
Diff to previous 1.27
fix off-by-one

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 1 19:27:39 2010 UTC (9 years, 4 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.26: +1 -1 lines
Diff to previous 1.26
add id to diagnostic

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 1 19:25:34 2010 UTC (9 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.25: +2 -2 lines
Diff to previous 1.25
update for 8-digit kmers

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 1 20:29:29 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.24: +10 -3 lines
Diff to previous 1.24
Fix nasty bug in hit thresholds

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 1 13:48:24 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.23: +1 -0 lines
Diff to previous 1.23
additional short-sequence fix

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 28 20:22:53 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.22: +2 -1 lines
Diff to previous 1.22
eliminate crash on very short sequences

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 28 19:12:11 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.21: +15 -0 lines
Diff to previous 1.21
kmer info changes

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 11 16:21:31 2010 UTC (9 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.20: +39 -6 lines
Diff to previous 1.20
Modifications for figfam calling.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 20 16:25:55 2010 UTC (9 years, 6 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0928
Changes since 1.19: +24 -2 lines
Diff to previous 1.19
Add support for -determineFamily and -familySims to assign_functions_to_prot_set

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 19 00:10:58 2010 UTC (10 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827
Changes since 1.18: +57 -22 lines
Diff to previous 1.18
Support constructor that takes friDB/setIDB/table.binary instead of a kmers dir.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 22 21:19:58 2009 UTC (10 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.17: +5 -0 lines
Diff to previous 1.17
assign_using_similarity: if passed an empty input, just return an empty output

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 19:32:29 2009 UTC (10 years, 3 months ago) by olson
Branch: MAIN
Changes since 1.16: +399 -170 lines
Diff to previous 1.16
mods for new server stuff

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 30 15:45:08 2009 UTC (10 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.15: +1 -0 lines
Diff to previous 1.15
Added a confess for the case where there is no incoming sequence, in order to make it easier to trace the source of the problem.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 21 21:31:57 2009 UTC (10 years, 7 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2009_0925
Changes since 1.14: +119 -9 lines
Diff to previous 1.14
Add assign_functions_to_prot_set.
Use ProtSims::blastP instead of blast for protein assignments when an extra db is given.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Jun 28 03:23:49 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.13: +58 -14 lines
Diff to previous 1.13
minor fixes

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jun 20 21:35:07 2009 UTC (10 years, 9 months ago) by overbeek
Branch: MAIN
Changes since 1.12: +29 -2 lines
Diff to previous 1.12
fixes to support Kmer analysis

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 4 21:24:25 2009 UTC (10 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.11: +172 -142 lines
Diff to previous 1.11
Support for OTUs.

Support for new C interface.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 26 18:23:33 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.10: +109 -18 lines
Diff to previous 1.10
fixes to support blasting against rRNAs

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 22 17:32:58 2009 UTC (10 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
if no blast requested, return empty list of blast hits

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 19 02:38:56 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2009_05_18
Changes since 1.8: +1 -1 lines
Diff to previous 1.8
fix blast to add ln2

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 18 19:36:49 2009 UTC (10 years, 10 months ago) by overbeek
Branch: MAIN
Changes since 1.7: +47 -19 lines
Diff to previous 1.7
support blast in Kmer searches

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 11 20:55:05 2009 UTC (10 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.6: +11 -8 lines
Diff to previous 1.6
Parameterize assign_functions_to_DNA to add $min_hits (default to 3) and $max_gap (default to 600) arguments.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sat May 9 00:02:11 2009 UTC (10 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.5: +54 -24 lines
Diff to previous 1.5
make sure extension is conservative

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 5 18:48:36 2009 UTC (10 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.4: +3 -1 lines
Diff to previous 1.4
fix for new version

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 28 19:42:10 2009 UTC (10 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.3: +3 -3 lines
Diff to previous 1.3
open ties readonly

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 23 21:02:48 2009 UTC (10 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.2: +79 -10 lines
Diff to previous 1.2
add support for the KmersC accelerated lookup code.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 20 20:31:33 2009 UTC (10 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +1 -1 lines
Diff to previous 1.1
change assign_function_to_DNA to assign_functions_to_DNA

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 20 18:52:05 2009 UTC (10 years, 11 months ago) by overbeek
Branch: MAIN
initial Kmer processing code

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