Commits · 73236c72a85da621a32a39bef008f05c61c9a333 · OBITools / ecoprimers

22 Jan, 2019 1 commit
- version 0.5: ecoPrimers can now read *.ldx files (local taxa) · 73236c72
  Celine Mercier authored Jan 22, 2019
  
  73236c72
29 Nov, 2017 3 commits
- Switch to version 0.4 · eb8d4452
  Celine Mercier authored Nov 29, 2017
  
  eb8d4452
- Changed the behaviour if trying to realloc a memory chunk of size 0 to · 2b3a3316
  Celine Mercier authored Nov 29, 2017
```
be consistent across systems (an error would be generated on Ubuntu when
no primers found)
```
  2b3a3316
- Moved the print of an error so the program does not abort before it is · a75191bb
  Celine Mercier authored Nov 29, 2017
```
printed
```
  a75191bb
17 Jul, 2015 1 commit
- clean *.P with Makefile · 3cfbf8ba
  Celine Mercier authored Jul 17, 2015
  
  3cfbf8ba
14 May, 2012 1 commit
- MOD : error in the stop condition in a for loop when printing results (may lead to a segv) · 66c0511f
  Frédéric Boyer authored May 14, 2012
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@420 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  66c0511f
27 Apr, 2012 2 commits

Frédéric Boyer authored Apr 27, 2012

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@413 60f365c0-8329-0410-b2a4-ec073aeeaa1d

ea1ca1b6

REMOVE libapat · 58a65f7f

Frédéric Boyer authored Apr 27, 2012

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@412 60f365c0-8329-0410-b2a4-ec073aeeaa1d

58a65f7f

26 Apr, 2012 1 commit
- ADD libapat so that everything is included when fetching the project from svn · 4315aecb
  Frédéric Boyer authored Apr 26, 2012
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@411 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  4315aecb
29 Feb, 2012 1 commit

Added some comments · aedee0c1

Frédéric Boyer authored Feb 29, 2012

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@400 60f365c0-8329-0410-b2a4-ec073aeeaa1d

aedee0c1

27 Feb, 2012 1 commit

Added some comments · 9e36754f

Frédéric Boyer authored Feb 27, 2012

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@399 60f365c0-8329-0410-b2a4-ec073aeeaa1d

9e36754f

22 Feb, 2012 1 commit

added "include <stdlib.h>" · 9262e954

Frédéric Boyer authored Feb 22, 2012

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@398 60f365c0-8329-0410-b2a4-ec073aeeaa1d

9262e954

03 Jan, 2012 1 commit
- My complete changes on my laptop, with specificity bug fix + ahocorasick + sets · 1f5a30b0
  Eric Coissac authored Jan 03, 2012
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@393 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  1f5a30b0
09 May, 2011 1 commit

updated makefile, changed project name · 19887e9a

Eric Coissac authored May 09, 2011

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@295 60f365c0-8329-0410-b2a4-ec073aeeaa1d

19887e9a

16 Dec, 2010 1 commit

fixed segmentation fault reported by Pierre. · 4c9c8382

Eric Coissac authored Dec 16, 2010

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@289 60f365c0-8329-0410-b2a4-ec073aeeaa1d

4c9c8382

13 Dec, 2010 1 commit
- added check for filtering pairs having specificity below a given threshold given using -T option · 5d8103f4
  Eric Coissac authored Dec 13, 2010
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@288 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  5d8103f4
29 Nov, 2010 1 commit

fixed specificity and pairing bugs · ca1e9d88

Eric Coissac authored Nov 29, 2010

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@287 60f365c0-8329-0410-b2a4-ec073aeeaa1d

ca1e9d88

13 Sep, 2010 1 commit
- Added code for building sets of primers and -p command line option · dd08d73d
  Eric Coissac authored Sep 13, 2010
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@279 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  dd08d73d
30 Aug, 2010 3 commits

Patch average size of amplicon computation · e483b17e

Eric Coissac authored Aug 30, 2010

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@275 60f365c0-8329-0410-b2a4-ec073aeeaa1d

e483b17e

Patch average size of amplicon computation · 396d6e20

Eric Coissac authored Aug 30, 2010

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@274 60f365c0-8329-0410-b2a4-ec073aeeaa1d

396d6e20

Patch stat output · 3f488baa

Eric Coissac authored Aug 30, 2010

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@273 60f365c0-8329-0410-b2a4-ec073aeeaa1d

3f488baa

25 Aug, 2010 2 commits

Add sequence length in database list output (option -A) · fd137882

Eric Coissac authored Aug 25, 2010

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@270 60f365c0-8329-0410-b2a4-ec073aeeaa1d

fd137882

Add sequence length in database list output (option -A) · 82d5e214

Eric Coissac authored Aug 25, 2010

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@269 60f365c0-8329-0410-b2a4-ec073aeeaa1d

82d5e214

15 Jun, 2010 1 commit

Revert previous commit · 0f4f2a74

Eric Coissac authored Jun 15, 2010

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@261 60f365c0-8329-0410-b2a4-ec073aeeaa1d

0f4f2a74

07 Apr, 2010 1 commit

· b3d6acae

Eric Coissac authored Apr 07, 2010

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@256 60f365c0-8329-0410-b2a4-ec073aeeaa1d

b3d6acae

09 Nov, 2009 1 commit

Patch taxon example/counterexample selection · 89576b96

Eric Coissac authored Nov 09, 2009

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@237 60f365c0-8329-0410-b2a4-ec073aeeaa1d

89576b96

19 Oct, 2009 2 commits
- Add a new option -E to considere some example sequences as counterexamples · 9e6b924c
  Eric Coissac authored Oct 19, 2009
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@236 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  9e6b924c
- Add a new option -E to considere some example sequences as counterexamples · 2737cf06
  Eric Coissac authored Oct 19, 2009
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@235 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  2737cf06
12 Oct, 2009 1 commit

Change 1 : patch the help message to take into account option added and the new output format. · 6f5f2a16

Eric Coissac authored Oct 12, 2009

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

6f5f2a16

31 Jul, 2009 1 commit

fixed a small problem of operator precedence in "if (w1 ^ w1a != 0) continue;"... · 088b5c09

Eric Coissac authored Jul 31, 2009

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

088b5c09

30 Jul, 2009 2 commits

corrected mask bits for base pairs · f1f85629

Eric Coissac authored Jul 30, 2009

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@232 60f365c0-8329-0410-b2a4-ec073aeeaa1d

f1f85629

Added Code to make sure that if -3 option is given then 3' end must match upto... · 1911880b

Eric Coissac authored Jul 30, 2009

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

1911880b

28 Jul, 2009 1 commit

Reintroduce -3 options to allow strict match at 3' end · 494791d1

Eric Coissac authored Jul 28, 2009

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@230 60f365c0-8329-0410-b2a4-ec073aeeaa1d

494791d1

18 Jul, 2009 2 commits

Patch minimum tm computation to limit estimation on example sequences · 79cadf08
Eric Coissac authored Jul 18, 2009
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@229 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
79cadf08

Patch minimum tm computation · 419bda96

Eric Coissac authored Jul 18, 2009

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

419bda96

17 Jul, 2009 3 commits

Deleted some supurious files · 455bf639

Eric Coissac authored Jul 17, 2009

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@227 60f365c0-8329-0410-b2a4-ec073aeeaa1d

455bf639

Committed thermostats.c · b625941d

Eric Coissac authored Jul 17, 2009

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@226 60f365c0-8329-0410-b2a4-ec073aeeaa1d

b625941d

committed thermostats.h · ba26734e

Eric Coissac authored Jul 17, 2009

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@225 60f365c0-8329-0410-b2a4-ec073aeeaa1d

ba26734e

14 Jul, 2009 1 commit

Added command line options for: · 50c26e81

Eric Coissac authored Jul 14, 2009

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

50c26e81

13 Jul, 2009 1 commit

commit -m "Cleaned code for thermodynamics properties and added Melting... · e79738e1

Eric Coissac authored Jul 13, 2009

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

e79738e1