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Author SHA1 Message Date
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
coissac 6624181788 remove *.P files 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@209 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-05-12 09:13:13 +00:00
coissac 81ada091bf Add option to log memory statistics during primer identifications 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@208 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-05-12 09:06:43 +00:00
coissac c5a430ea80 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@207 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2009-04-28 21:20:20 +00:00
coissac c308fb2edc Patch eco_malloc functions to allow more than 4Gb allocation on 64bits version 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@206 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-04-28 08:19:50 +00:00
coissac 796274d746 some patches to compile on linux 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@205 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-04-23 22:22:27 +00:00
coissac c36bc5e838 Second run of patch 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@204 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-04-23 11:38:52 +00:00
coissac 313dd59f5a First run of patch 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@203 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-04-22 08:15:18 +00:00
coissac e869d6daed git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@202 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2009-04-20 08:40:32 +00:00
coissac 93b327285a git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@201 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2009-04-20 08:40:14 +00:00
coissac e3d922e103 Merge of eric-test branche to the trunk 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@200 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-04-20 08:38:41 +00:00
coissac b8af5dd65f Merge of eric-test branche to the trunk 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@199 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-04-20 08:31:30 +00:00
coissac 4f9d76f0f2 New version based on sort them merge algorithm 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@182 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-03-04 22:37:58 +00:00
coissac b5b0ca7e9d git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@181 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2009-03-04 22:35:06 +00:00
coissac 64838c1cdf New version based on sort them merge algorithm 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@180 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-03-04 22:32:55 +00:00
coissac 6d8bb449d5 delete old version 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@179 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-03-04 22:22:48 +00:00
coissac f9410e5aee Initial commit for this soft 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@175 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-10-13 10:39:14 +00:00
coissac f5abbabb54 initial project 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@172 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-10-13 09:45:11 +00:00