obitools/ecopcr
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58 Commits 2 Branches 6 Tags
3503f66520644124a96be8089fa78d0558dfea07
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Author SHA1 Message Date
Eric Coissac
3503f66520 Update ecopcr.c to comment a debug message 2020-04-27 14:10:30 +02:00
Eric Coissac
9deb30a8c4 Patch a bug inducing that sequences were considered as circular whatever 
the -c option was present or not.
 2020-04-27 12:07:28 +02:00
Celine Mercier
c4321036be Fixed length computation bug introduced in last version ecopcr_v1.0.1 2019-01-22 15:17:59 +01:00
Celine Mercier
a92a7fa070 Fixed version + some git ignore things 2018-07-30 14:45:48 +02:00
Celine Mercier
bd1db764d4 Fixed a bug when primers would touch or overlap, producing amplicons of 
size <= 0
ecopcr_v1.0.0 		2018-07-26 19:03:59 +02:00
Celine Mercier
f0cca648ea Version 0.8.0 ecopcr_v0.8.0 2017-02-06 14:34:57 +01:00
Celine Mercier
573bd5bad7 Removed deprecated code in ecoPCRFormat 2017-02-06 11:24:32 +01:00
Celine Mercier
17387dae8d Deleted OS X code specificities ecopcr_v0.7.0 2017-02-03 13:56:32 +01:00
Celine Mercier
18583c4d2e Changed compilation flags and fixed typo in ecoPCR help 2017-02-03 11:36:36 +01:00
Celine Mercier
2dd4a217f1 Merge branch 'master' of https://git.metabarcoding.org/obitools/ecopcr ecopcr_v0.6.0 2017-02-01 17:12:18 +01:00
Celine Mercier
9a0d77535f Fixing versioning problem with new version 0.6.0 2017-02-01 16:50:07 +01:00
Eric Coissac
b09bd1455b Add license 2017-01-11 13:01:41 +01:00
Celine Mercier
194ec811f4 Fixes #2 by adding the missing -D option in the help ecopcr_v0.5.0 2015-05-19 13:52:35 +02:00
Eric Coissac
126bf80670 Convert svn:ignore properties to .gitignore. 2015-05-16 17:51:46 +02:00
Frédéric Boyer
46d086b215 unsufficient space allocated for handling strings in arguments 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@595 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2013-03-07 09:25:16 +00:00
Frédéric Boyer
0a62ff49cc MOD: updated the help to include the -P option 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@424 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-05-16 11:56:36 +00:00
Frédéric Boyer
2452df90de MOD: Added a [P]ath option displaying for each taxon its full path 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@423 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-05-16 11:43:33 +00:00
Frédéric Boyer
745d50cfa4 MOD: Corrected condition in getSon to handle the root of the taxonomy 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@422 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-05-16 07:52:28 +00:00
Eric Coissac
e2fe83fcb7 remove extra obitools directory from ecoPCR subversion archive 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@418 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-05-07 09:31:08 +00:00
Frédéric Boyer
2a118eedda MOD: In the printRepeat function, corrected rdelta and ldelta management 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@417 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-05-07 09:14:09 +00:00
Céline Mercier
93c530e090 removed the "without temperature" option 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@416 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2012-05-04 14:53:33 +00:00
Eric Coissac
4e5d8893e5 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@390 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2011-12-05 12:59:34 +00:00
Eric Coissac
957a59eb5d Add management of local taxa from the new extension of the OBI Taxonomy library 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@315 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2011-07-19 06:44:47 +00:00
Eric Coissac
9adf426abf delta bug 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@310 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2011-06-30 15:26:36 +00:00
Eric Coissac
ae528e48f4 delta bug 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@309 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2011-06-30 15:12:38 +00:00
Eric Coissac
f53cc6d500 patch on printing 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@299 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2011-06-15 21:54:33 +00:00
Eric Coissac
8313c67a9b syntax debug on ecopcr.c 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@297 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2011-05-25 16:35:30 +00:00
Eric Coissac
01173d22cf add an hidden -D option 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@296 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2011-05-25 15:41:22 +00:00
Eric Coissac
87c2496447 patch a bug in Tm computation 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@260 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-05-23 12:30:16 +00:00
Eric Coissac
9867859237 patch for 64bits constants 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@244 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-02-24 15:10:11 +00:00
Eric Coissac
f6f39f58fe patch Tm calculation to return NaN if one of the two sequence is composed with letters different than ACGT 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@243 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-02-24 15:00:11 +00:00
Eric Coissac
7331dd5612 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@242 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2010-01-22 09:21:04 +00:00
Eric Coissac
0214be011e git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@241 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2010-01-22 09:20:09 +00:00
Eric Coissac
1c30a8604f git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@240 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2010-01-22 09:19:36 +00:00
Eric Coissac
985d067bd8 New version 0.2 of ecoPCR, with Tm computation. 
Take care file format have change. You must use corresponding version of ecogrep
You can use -t option to go back to the old format without tm computation

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@239 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-01-22 09:19:19 +00:00
Eric Coissac
f7e25b2082 New version 0.2 of ecoPCR, with Tm computation. 
Take care file format have change. You must use corresponding version of ecogrep
You can use -t option to go back to the old format without tm computation

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@238 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-01-22 09:16:53 +00:00
Eric Coissac
ad6f493d0f Accept to deal with sequence in lower case 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@217 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-05-13 13:21:10 +00:00
Eric Coissac
1428cd7499 patch online help in ecoPCR software 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@168 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-05-16 08:53:11 +00:00
Eric Coissac
708b7c387e Sequence circularity, bug correction 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@167 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-04-28 16:46:18 +00:00
Eric Coissac
d863b7e48e Manage sequence circularity 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@166 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-04-28 15:49:12 +00:00
Eric Coissac
4b74056af8 change reference column for taxonomy filtering in ecogrep.c 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@165 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-03-12 21:26:08 +00:00
Eric Coissac
f68f4af244 Add option to ecoPCRFormat to deal with an obischema db as taxonomy source 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@158 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-02-08 10:27:42 +00:00
Eric Coissac
a1141a77b5 -- 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@119 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-09-24 10:10:03 +00:00
Eric Coissac
6835206344 Add version file 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@118 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-09-24 10:07:39 +00:00
Eric Coissac
45c85a9f32 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@117 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2007-09-24 10:06:00 +00:00
Eric Coissac
471bf72bf9 Add rule for ecogrep build in makefile 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@116 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-09-24 09:58:48 +00:00
Eric Coissac
22ecb4b842 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@115 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2007-09-24 09:48:19 +00:00
Eric Coissac
bc4c7656c6 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@114 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2007-09-24 09:48:08 +00:00
Eric Coissac
6cd1141130 Add capacity to format fasta files, with taxonomical data described in title line in the following format : 
[taxon: ####] where #### is a taxid from NCBI taxonomy. It can be as precise as possible (species, genus or even root)
		

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@13 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-05-02 10:10:27 +00:00
Eric Coissac
420cdb877b add a -k option to the ecoPCR binary to substitute superkingdom column by a kingdom column 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@12 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-03-27 16:33:50 +00:00