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Author SHA1 Message Date
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
Eric Coissac
b4d8842f31 Add minus -R option to localize aplicon over one of the sequence database. 
This option add two column on the right of the output table with the primers location 
and the barcode sequence (small patch)

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@220 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-06-24 08:12:50 +00:00
Eric Coissac
1cae92e963 Add minus -R option to localize aplicon over one of the sequence database. 
This option add two column on the right of the output table with the primers location 
and the barcode sequence    

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@219 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-06-24 08:09:39 +00:00
Eric Coissac
3a617890ca New option for reference sequence 
and bug correction for insequence count

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@218 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-06-23 14:11:39 +00:00
Eric Coissac
40644bc85f git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@216 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2009-05-13 09:26:57 +00:00
Eric Coissac
c192908469 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@215 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2009-05-13 09:18:24 +00:00
Eric Coissac
b0521a7e15 Accept to deal with sequence in lower case 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@214 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-05-13 07:33:39 +00:00
Eric Coissac
b7c1640042 New version 0.3 with filtering on short words 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@213 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-05-13 06:51:25 +00:00
Eric Coissac
5dc55c7f53 Some linux patch 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@212 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-05-12 15:48:59 +00:00
Eric Coissac
04ee4e531c remove final binary from archive 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@211 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-05-12 09:17:52 +00:00
Eric Coissac
b092497eaf add property to ignore *.P files 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@210 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-05-12 09:16:09 +00:00