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08debff2acd645417c7217cc59c74b230fad1535
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Author SHA1 Message Date
coissac
08debff2ac Actualiser src/Makefile 2025-06-12 08:35:23 +00:00
coissac
e16e9bfa0c Actualiser src/global.mk 2025-06-12 08:34:54 +00:00
Eric Coissac
7fbea9d63f adds the binary to the gitignore 2024-05-24 14:27:17 +02:00
Eric Coissac
9a9fb383ad standardize uint type names 2024-05-24 14:26:22 +02:00
Eric Coissac
8c1668faa4 patch some compile warnings 2024-05-23 17:46:00 +02:00
Eric Coissac
92826de147 Update to consider evolution of the language 2023-06-29 12:12:46 +02:00
Celine Mercier
73236c72a8 version 0.5: ecoPrimers can now read *.ldx files (local taxa) ecoprimers_v0.5 2019-01-22 15:51:43 +01:00
Celine Mercier
eb8d44528d Switch to version 0.4 ecoprimers_v0.4 2017-11-29 14:38:23 +01:00
Celine Mercier
2b3a331602 Changed the behaviour if trying to realloc a memory chunk of size 0 to 
be consistent across systems (an error would be generated on Ubuntu when
no primers found)
 2017-11-29 14:25:14 +01:00
Celine Mercier
a75191bbe6 Moved the print of an error so the program does not abort before it is 
printed
 2017-11-29 10:46:48 +01:00
Celine Mercier
3cfbf8ba42 clean *.P with Makefile 2015-07-17 15:48:35 +02:00
Eric Coissac
efb4fba78c Convert svn:ignore properties to .gitignore. 2015-05-16 23:45:29 +02:00
Frédéric Boyer
66c0511f09 MOD : error in the stop condition in a for loop when printing results (may lead to a segv) 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@420 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-05-14 13:02:44 +00:00
Frédéric Boyer
ea1ca1b6d9 Modified LIBPATH 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@413 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-04-27 06:53:47 +00:00
Frédéric Boyer
58a65f7ff4 REMOVE libapat 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@412 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-04-27 06:50:22 +00:00
Frédéric Boyer
4315aecbf0 ADD libapat so that everything is included when fetching the project from svn 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@411 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-04-26 16:23:35 +00:00
Frédéric Boyer
aedee0c154 Added some comments 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@400 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-02-29 14:12:17 +00:00
Frédéric Boyer
9e36754fef Added some comments 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@399 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-02-27 14:57:03 +00:00
Frédéric Boyer
9262e954cf added "include <stdlib.h>" 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@398 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-02-22 11:25:30 +00:00
Eric Coissac
1f5a30b0df My complete changes on my laptop, with specificity bug fix + ahocorasick + sets 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@393 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-01-03 21:05:31 +00:00
Eric Coissac
19887e9a46 updated makefile, changed project name 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@295 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2011-05-09 13:13:24 +00:00
Eric Coissac
e77c6e5339 updated version 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@291 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2011-02-04 23:46:02 +00:00
Eric Coissac
4c9c8382fe fixed segmentation fault reported by Pierre. 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@289 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-12-16 20:56:57 +00:00
Eric Coissac
5d8103f4b4 added check for filtering pairs having specificity below a given threshold given using -T option 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@288 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-12-13 17:09:54 +00:00
Eric Coissac
ca1e9d8899 fixed specificity and pairing bugs 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@287 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-11-29 22:57:56 +00:00
Eric Coissac
dd08d73dda Added code for building sets of primers and -p command line option 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@279 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-09-13 09:44:53 +00:00
Eric Coissac
e483b17e18 Patch average size of amplicon computation 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@275 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-08-30 12:14:40 +00:00
Eric Coissac
396d6e2028 Patch average size of amplicon computation 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@274 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-08-30 12:13:54 +00:00
Eric Coissac
3f488baa6f Patch stat output 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@273 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-08-30 12:13:28 +00:00
Eric Coissac
fd13788289 Add sequence length in database list output (option -A) 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@270 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-08-25 12:59:30 +00:00
Eric Coissac
82d5e21471 Add sequence length in database list output (option -A) 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@269 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-08-25 12:55:58 +00:00
Eric Coissac
0f4f2a74fe Revert previous commit 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@261 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-06-15 05:03:20 +00:00
Eric Coissac
b3d6acae76 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@256 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2010-04-07 11:32:41 +00:00
Eric Coissac
89576b96fa Patch taxon example/counterexample selection 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@237 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-11-09 14:50:35 +00:00
Eric Coissac
9e6b924c92 Add a new option -E to considere some example sequences as counterexamples 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@236 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-10-19 17:27:51 +00:00
Eric Coissac
2737cf0606 Add a new option -E to considere some example sequences as counterexamples 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@235 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-10-19 17:24:46 +00:00
Eric Coissac
6f5f2a16f3 Change 1 : patch the help message to take into account option added and the new output format. 
Change 2 : Change the used rules to define example and counter example taxon sets.
			By default all taxa are example taxa and no counterexample taxa are used.
			By using -r option (one or several time) you could restict example taxa to a subset of taxa
			In old version all taxa not in example set are in the counterexample set.
			Now restrict example set with -r option doesn't define the counter example set.
			You must use -i to define the conterexample set in a similar way or -r option for example taxa.  

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@234 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-10-12 13:31:41 +00:00
Eric Coissac
088b5c09d0 fixed a small problem of operator precedence in "if (w1 ^ w1a != 0) continue;" by adding parentheses. 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@233 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-31 09:52:04 +00:00
Eric Coissac
f1f8562918 corrected mask bits for base pairs 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@232 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-30 22:30:04 +00:00
Eric Coissac
1911880bb9 Added Code to make sure that if -3 option is given then 3' end must match upto given number of base pairs 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@231 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-30 22:20:07 +00:00
Eric Coissac
494791d133 Reintroduce -3 options to allow strict match at 3' end 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@230 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-28 21:07:27 +00:00
Eric Coissac
79cadf0809 Patch minimum tm computation to limit estimation on example sequences 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@229 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-18 22:33:18 +00:00
Eric Coissac
419bda966d Patch minimum tm computation 
Add -A option to list all id present in the DB for helping in -R usage

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@228 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-18 22:16:18 +00:00
Eric Coissac
455bf63949 Deleted some supurious files 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@227 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-17 22:29:19 +00:00
Eric Coissac
b625941d72 Committed thermostats.c 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@226 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-17 22:11:40 +00:00
Eric Coissac
ba26734e9b committed thermostats.h 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@225 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-17 15:02:12 +00:00
Eric Coissac
50c26e81b9 Added command line options for: 
a. 'salt method' like "-m 1" or "-m 2" here 1 is for SANTALUCIA and 2 is for OWCZARZY
b. 'salt concentration' "-a 0.01" valid range is from 0.01 to 0.3. if not specified then we use default 0.05

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@224 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-14 22:23:18 +00:00
Eric Coissac
e79738e170 commit -m "Cleaned code for thermodynamics properties and added Melting Temperature for approximate version of strict repeats. Also cleaned printing code. 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@223 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-13 09:26:19 +00:00
Eric Coissac
91753ace82 Added thermodynamics properties 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@222 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-07 12:35:55 +00:00
Eric Coissac
f142d0e904 Added thermodynamics properties 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@221 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-07-07 12:35:17 +00:00