Commits · ca1e9d88994772732206928eebe64f21ba12bf29 · OBITools / ecoprimers

29 Nov, 2010 1 commit

fixed specificity and pairing bugs · ca1e9d88

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

committed Nov 29, 2010

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

Patch average size of amplicon computation · e483b17e

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

committed Aug 30, 2010

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Patch average size of amplicon computation · 396d6e20

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

committed Aug 30, 2010

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Patch stat output · 3f488baa

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

committed Aug 30, 2010

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25 Aug, 2010 2 commits
- Add sequence length in database list output (option -A) · fd137882
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@270 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  Eric Coissac committed Aug 25, 2010
  fd137882 Browse Files
- Add sequence length in database list output (option -A) · 82d5e214
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@269 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  Eric Coissac committed Aug 25, 2010
  82d5e214 Browse Files
15 Jun, 2010 1 commit

Revert previous commit · 0f4f2a74

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

committed Jun 15, 2010

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07 Apr, 2010 1 commit
- git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@256… · b3d6acae
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@256 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  Eric Coissac committed Apr 07, 2010
  b3d6acae Browse Files
09 Nov, 2009 1 commit

Patch taxon example/counterexample selection · 89576b96

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

committed Nov 09, 2009

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

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

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

committed Oct 12, 2009

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31 Jul, 2009 1 commit

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

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

committed Jul 31, 2009

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30 Jul, 2009 2 commits

corrected mask bits for base pairs · f1f85629

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

committed Jul 30, 2009

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

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

committed Jul 30, 2009

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28 Jul, 2009 1 commit
- Reintroduce -3 options to allow strict match at 3' end · 494791d1
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@230 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  Eric Coissac committed Jul 28, 2009
  494791d1 Browse Files
18 Jul, 2009 2 commits

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

Patch minimum tm computation · 419bda96

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

committed Jul 18, 2009

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17 Jul, 2009 3 commits

Deleted some supurious files · 455bf639

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

committed Jul 17, 2009

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Committed thermostats.c · b625941d

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

committed Jul 17, 2009

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committed thermostats.h · ba26734e

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

committed Jul 17, 2009

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14 Jul, 2009 1 commit

Added command line options for: · 50c26e81

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

committed Jul 14, 2009

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13 Jul, 2009 1 commit

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

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

committed Jul 13, 2009

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07 Jul, 2009 2 commits

Added thermodynamics properties · 91753ace

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@222 60f365c0-8329-0410-b2a4-ec073aeeaa1d

committed Jul 07, 2009

91753ace Browse Files

Added thermodynamics properties · f142d0e9

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@221 60f365c0-8329-0410-b2a4-ec073aeeaa1d

committed Jul 07, 2009

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24 Jun, 2009 2 commits

Add minus -R option to localize aplicon over one of the sequence database. · b4d8842f

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

committed Jun 24, 2009

b4d8842f Browse Files

Add minus -R option to localize aplicon over one of the sequence database. · 1cae92e9

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

committed Jun 24, 2009

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23 Jun, 2009 1 commit

New option for reference sequence · 3a617890

and bug correction for insequence count

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@218 60f365c0-8329-0410-b2a4-ec073aeeaa1d

committed Jun 23, 2009

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13 May, 2009 4 commits
- git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@216… · 40644bc8
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@216 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  Eric Coissac committed May 13, 2009
  40644bc8 Browse Files
- git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@215… · c1929084
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@215 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  Eric Coissac committed May 13, 2009
  c1929084 Browse Files
- Accept to deal with sequence in lower case · b0521a7e
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@214 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  Eric Coissac committed May 13, 2009
  b0521a7e Browse Files
- New version 0.3 with filtering on short words · b7c16400
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@213 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  Eric Coissac committed May 13, 2009
  b7c16400 Browse Files
12 May, 2009 5 commits

Some linux patch · 5dc55c7f

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@212 60f365c0-8329-0410-b2a4-ec073aeeaa1d

committed May 12, 2009

5dc55c7f Browse Files

remove final binary from archive · 04ee4e53

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@211 60f365c0-8329-0410-b2a4-ec073aeeaa1d

committed May 12, 2009

04ee4e53 Browse Files

add property to ignore *.P files · b092497e

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@210 60f365c0-8329-0410-b2a4-ec073aeeaa1d

committed May 12, 2009

b092497e Browse Files

remove *.P files · 66241817

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@209 60f365c0-8329-0410-b2a4-ec073aeeaa1d

committed May 12, 2009

66241817 Browse Files

Add option to log memory statistics during primer identifications · 81ada091
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@208 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
Eric Coissac committed May 12, 2009
81ada091 Browse Files

28 Apr, 2009 2 commits
- git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@207… · c5a430ea
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@207 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  Eric Coissac committed Apr 28, 2009
  c5a430ea Browse Files
- Patch eco_malloc functions to allow more than 4Gb allocation on 64bits version · c308fb2e
```
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@206 60f365c0-8329-0410-b2a4-ec073aeeaa1d
```
  Eric Coissac committed Apr 28, 2009
  c308fb2e Browse Files