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ecoPrimers-2.1

eric-test

kmr-version

master

ecoprimers_v0.4

ecoprimers_v0.5

Mono Color

• d4fa8b43a4 Actualiser src/global.mk master coissac 2025-06-12 14:22:23 +00:00
• b7552200bd Actualiser tools/ecoPCRFormat.py coissac 2025-06-12 13:58:59 +00:00
• 791aeb0ef9 Actualiser src/libecoPCR/ecotax.c coissac 2025-06-12 13:33:51 +00:00
• 1e3f82bb51 Actualiser src/libecoPCR/ecorank.c coissac 2025-06-12 13:32:53 +00:00
• f1ef2caae6 Supprimer tools/ecoPCRFormat23.py coissac 2025-06-12 13:29:57 +00:00
• 680cc4d7a2 Actualiser tools/ecoPCRFormat.py coissac 2025-06-12 13:29:46 +00:00
• 09f3e19f32 Ajouter tools/ecoPCRFormat23.py coissac 2025-06-12 08:53:59 +00:00
• 08debff2ac Actualiser src/Makefile coissac 2025-06-12 08:35:23 +00:00
• e16e9bfa0c Actualiser src/global.mk coissac 2025-06-12 08:34:54 +00:00
• 7fbea9d63f adds the binary to the gitignore Eric Coissac 2024-05-24 14:27:17 +02:00
• 9a9fb383ad standardize uint type names Eric Coissac 2024-05-24 14:26:22 +02:00
• 8c1668faa4 patch some compile warnings Eric Coissac 2024-05-23 17:46:00 +02:00
• 92826de147 Update to consider evolution of the language Eric Coissac 2023-06-29 12:12:46 +02:00
• 73236c72a8 version 0.5: ecoPrimers can now read *.ldx files (local taxa) ecoprimers_v0.5 Celine Mercier 2019-01-22 15:51:43 +01:00
• eb8d44528d Switch to version 0.4 ecoprimers_v0.4 Celine Mercier 2017-11-29 14:38:23 +01:00
• 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) Celine Mercier 2017-11-29 14:25:14 +01:00
• a75191bbe6 Moved the print of an error so the program does not abort before it is printed Celine Mercier 2017-11-29 10:46:48 +01:00
• 3cfbf8ba42 clean *.P with Makefile Celine Mercier 2015-07-17 15:48:35 +02:00
• b3d98e2e83 Fixes 1 ecoPrimers-2.1 Celine Mercier 2015-06-05 09:49:58 +02:00
• efb4fba78c Convert svn:ignore properties to .gitignore. Eric Coissac 2015-05-16 23:45:29 +02:00
• 66c0511f09 MOD : error in the stop condition in a for loop when printing results (may lead to a segv) Frédéric Boyer 2012-05-14 13:02:44 +00:00
• ea1ca1b6d9 Modified LIBPATH Frédéric Boyer 2012-04-27 06:53:47 +00:00
• 58a65f7ff4 REMOVE libapat Frédéric Boyer 2012-04-27 06:50:22 +00:00
• 4315aecbf0 ADD libapat so that everything is included when fetching the project from svn Frédéric Boyer 2012-04-26 16:23:35 +00:00
• aedee0c154 Added some comments Frédéric Boyer 2012-02-29 14:12:17 +00:00
• 9e36754fef Added some comments Frédéric Boyer 2012-02-27 14:57:03 +00:00
• 9262e954cf added "include <stdlib.h>" Frédéric Boyer 2012-02-22 11:25:30 +00:00
• 1f5a30b0df My complete changes on my laptop, with specificity bug fix + ahocorasick + sets Eric Coissac 2012-01-03 21:05:31 +00:00
• e2ebc357ee Backup with sets and ahocorasick Eric Coissac 2011-06-01 22:42:30 +00:00
• 19887e9a46 updated makefile, changed project name Eric Coissac 2011-05-09 13:13:24 +00:00
• e77c6e5339 updated version Eric Coissac 2011-02-04 23:46:02 +00:00
• 4c9c8382fe fixed segmentation fault reported by Pierre. Eric Coissac 2010-12-16 20:56:57 +00:00
• 5d8103f4b4 added check for filtering pairs having specificity below a given threshold given using -T option Eric Coissac 2010-12-13 17:09:54 +00:00
• ca1e9d8899 fixed specificity and pairing bugs Eric Coissac 2010-11-29 22:57:56 +00:00
• dd08d73dda Added code for building sets of primers and -p command line option Eric Coissac 2010-09-13 09:44:53 +00:00
• e483b17e18 Patch average size of amplicon computation Eric Coissac 2010-08-30 12:14:40 +00:00
• 396d6e2028 Patch average size of amplicon computation Eric Coissac 2010-08-30 12:13:54 +00:00
• 3f488baa6f Patch stat output Eric Coissac 2010-08-30 12:13:28 +00:00
• fd13788289 Add sequence length in database list output (option -A) Eric Coissac 2010-08-25 12:59:30 +00:00
• 82d5e21471 Add sequence length in database list output (option -A) Eric Coissac 2010-08-25 12:55:58 +00:00
• 0f4f2a74fe Revert previous commit Eric Coissac 2010-06-15 05:03:20 +00:00
• b3d6acae76 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@256 60f365c0-8329-0410-b2a4-ec073aeeaa1d Eric Coissac 2010-04-07 11:32:41 +00:00
• 89576b96fa Patch taxon example/counterexample selection Eric Coissac 2009-11-09 14:50:35 +00:00
• 9e6b924c92 Add a new option -E to considere some example sequences as counterexamples Eric Coissac 2009-10-19 17:27:51 +00:00
• 2737cf0606 Add a new option -E to considere some example sequences as counterexamples Eric Coissac 2009-10-19 17:24:46 +00:00
• 6f5f2a16f3 Change 1 : patch the help message to take into account option added and the new output format. Eric Coissac 2009-10-12 13:31:41 +00:00
• 088b5c09d0 fixed a small problem of operator precedence in "if (w1 ^ w1a != 0) continue;" by adding parentheses. Eric Coissac 2009-07-31 09:52:04 +00:00
• f1f8562918 corrected mask bits for base pairs Eric Coissac 2009-07-30 22:30:04 +00:00
• 1911880bb9 Added Code to make sure that if -3 option is given then 3' end must match upto given number of base pairs Eric Coissac 2009-07-30 22:20:07 +00:00
• 494791d133 Reintroduce -3 options to allow strict match at 3' end Eric Coissac 2009-07-28 21:07:27 +00:00
• 79cadf0809 Patch minimum tm computation to limit estimation on example sequences Eric Coissac 2009-07-18 22:33:18 +00:00
• 419bda966d Patch minimum tm computation Add -A option to list all id present in the DB for helping in -R usage Eric Coissac 2009-07-18 22:16:18 +00:00
• 455bf63949 Deleted some supurious files Eric Coissac 2009-07-17 22:29:19 +00:00
• b625941d72 Committed thermostats.c Eric Coissac 2009-07-17 22:11:40 +00:00
• ba26734e9b committed thermostats.h Eric Coissac 2009-07-17 15:02:12 +00:00
• 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 Eric Coissac 2009-07-14 22:23:18 +00:00
• e79738e170 commit -m "Cleaned code for thermodynamics properties and added Melting Temperature for approximate version of strict repeats. Also cleaned printing code. Eric Coissac 2009-07-13 09:26:19 +00:00
• 91753ace82 Added thermodynamics properties Eric Coissac 2009-07-07 12:35:55 +00:00
• f142d0e904 Added thermodynamics properties Eric Coissac 2009-07-07 12:35:17 +00:00
• 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) Eric Coissac 2009-06-24 08:12:50 +00:00
• 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 Eric Coissac 2009-06-24 08:09:39 +00:00
• 3a617890ca New option for reference sequence and bug correction for insequence count Eric Coissac 2009-06-23 14:11:39 +00:00
• 40644bc85f git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@216 60f365c0-8329-0410-b2a4-ec073aeeaa1d Eric Coissac 2009-05-13 09:26:57 +00:00
• c192908469 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@215 60f365c0-8329-0410-b2a4-ec073aeeaa1d Eric Coissac 2009-05-13 09:18:24 +00:00
• b0521a7e15 Accept to deal with sequence in lower case Eric Coissac 2009-05-13 07:33:39 +00:00
• b7c1640042 New version 0.3 with filtering on short words Eric Coissac 2009-05-13 06:51:25 +00:00
• 5dc55c7f53 Some linux patch Eric Coissac 2009-05-12 15:48:59 +00:00
• 04ee4e531c remove final binary from archive Eric Coissac 2009-05-12 09:17:52 +00:00
• b092497eaf add property to ignore *.P files Eric Coissac 2009-05-12 09:16:09 +00:00
• 6624181788 remove *.P files Eric Coissac 2009-05-12 09:13:13 +00:00
• 81ada091bf Add option to log memory statistics during primer identifications Eric Coissac 2009-05-12 09:06:43 +00:00
• c5a430ea80 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@207 60f365c0-8329-0410-b2a4-ec073aeeaa1d Eric Coissac 2009-04-28 21:20:20 +00:00
• c308fb2edc Patch eco_malloc functions to allow more than 4Gb allocation on 64bits version Eric Coissac 2009-04-28 08:19:50 +00:00
• 796274d746 some patches to compile on linux Eric Coissac 2009-04-23 22:22:27 +00:00
• c36bc5e838 Second run of patch Eric Coissac 2009-04-23 11:38:52 +00:00
• 313dd59f5a First run of patch Eric Coissac 2009-04-22 08:15:18 +00:00
• e869d6daed git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@202 60f365c0-8329-0410-b2a4-ec073aeeaa1d Eric Coissac 2009-04-20 08:40:32 +00:00
• 93b327285a git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@201 60f365c0-8329-0410-b2a4-ec073aeeaa1d Eric Coissac 2009-04-20 08:40:14 +00:00
• e3d922e103 Merge of eric-test branche to the trunk Eric Coissac 2009-04-20 08:38:41 +00:00
• b8af5dd65f Merge of eric-test branche to the trunk Eric Coissac 2009-04-20 08:31:30 +00:00
• 68c4743303 added print help eric-test Eric Coissac 2009-04-14 11:06:26 +00:00
• 035495b2a1 fixed twalk action Eric Coissac 2009-03-26 15:15:08 +00:00
• 3c21789533 Removed some problems for specificity Eric Coissac 2009-03-26 00:22:01 +00:00
• 75a6dac09a git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/eric-test@195 60f365c0-8329-0410-b2a4-ec073aeeaa1d Eric Coissac 2009-03-25 10:18:34 +00:00
• 6726294c78 Removed compilation errors and added new implementation of ecoComplementChar Eric Coissac 2009-03-22 17:44:59 +00:00
• 584d3c406d added compare function for amplifias Eric Coissac 2009-03-20 11:59:55 +00:00
• 0440b8d761 Switch strict_three_prime option default value to 0 as a workaround bug patch Eric Coissac 2009-03-18 10:04:20 +00:00
• db061fbb12 Patch print function for reverse primer Eric Coissac 2009-03-17 10:44:00 +00:00
• ac52f3303d with full coverage statistic Eric Coissac 2009-03-15 21:53:24 +00:00
• 29820c1e26 with full coverage statistic Eric Coissac 2009-03-15 21:52:57 +00:00
• 5d212d5753 with full coverage statistic Eric Coissac 2009-03-15 21:52:29 +00:00
• 9908a40aaa with full coverage statistic Eric Coissac 2009-03-15 21:52:06 +00:00
• 665b22989f first version with preliminary print function Eric Coissac 2009-03-12 09:55:01 +00:00
• d911d6bd20 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/eric-test@185 60f365c0-8329-0410-b2a4-ec073aeeaa1d Eric Coissac 2009-03-10 08:49:11 +00:00
• dffebd5826 New version of pairing algorithm (alpha) Eric Coissac 2009-03-09 11:05:51 +00:00
• 2be5f2659b algo change test for eric Eric Coissac 2009-03-06 07:25:02 +00:00
• 4f9d76f0f2 New version based on sort them merge algorithm Eric Coissac 2009-03-04 22:37:58 +00:00
• b5b0ca7e9d git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@181 60f365c0-8329-0410-b2a4-ec073aeeaa1d Eric Coissac 2009-03-04 22:35:06 +00:00
• 64838c1cdf New version based on sort them merge algorithm Eric Coissac 2009-03-04 22:32:55 +00:00
• 6d8bb449d5 delete old version Eric Coissac 2009-03-04 22:22:48 +00:00