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Author SHA1 Message Date
coissac 8f0462c407 Merge branch 'master' into Eric_version_for_sequence 
Conflicts:
	python/obitools3/obidms/_obidmscolumn_seq.pyx
 2016-08-03 10:09:20 +02:00
coissac 000b9999ad Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-07-03 09:22:22 +02:00
coissac aff9831c13 Substitute fprintf call by fputs call to conform with the new ubuntu 
compilation rules
 2016-07-03 09:21:56 +02:00
coissac 448fa8d325 first trial for a fasta formater 2016-07-03 09:18:52 +02:00
coissac 6af62d8124 Change a fprintf without argument to a fputs to comply with the new 
default parameter on ubuntu
 2016-07-03 08:25:06 +02:00
coissac bac7ce7184 Start of the implementation of the export methods 2016-06-02 19:10:33 +02:00
coissac f186395661 Trap potential exception generated by char* to bytes casts 2016-05-29 21:18:20 +02:00
coissac 85395dfc1a value returned for sequence is now bytes and no more str 2016-05-29 13:53:32 +02:00
coissac f830389974 Add some comment on the location of the align method. 2016-05-29 12:58:31 +02:00
coissac 2e35229357 Add conversion checking on the value of a seq column 2016-05-29 12:54:13 +02:00
coissac a8ed57dc6e few small changes 2016-05-21 12:29:55 +02:00
coissac c3274d419c remove an extra debug log 2016-05-21 12:29:08 +02:00
coissac cca0dbb46b Close issue #54 by adding a read1 method to the MagicKeyFile class 2016-05-21 12:24:48 +02:00
coissac 5a78157112 increase parsing speed of the header 2016-05-21 10:29:11 +02:00
coissac 0b9a41d952 Patch a bug about the reading of the last sequence 2016-05-21 10:28:03 +02:00
coissac ef1be141c1 Update Licence to english version 2016-04-23 18:03:50 +02:00
coissac bbfd40d56d Add license 2016-04-23 18:03:10 +02:00
coissac 6fe4c6134a Allows for calling getConfiguration without parametter for geting the 
default configuration
 2016-04-11 13:31:09 +02:00
coissac 45c9c5075c A first version of the fasta parser 2016-04-01 18:15:54 +02:00
coissac 20b97c972b Add boolean type in the tag evaluation 2016-04-01 13:42:24 +02:00
coissac efc4a4a3c6 Reduce the call count to eval. This reduce by 3 the time of fast(q|a) 
header processing
 2016-04-01 08:54:06 +02:00
coissac ce6ea89c21 Add the missing bootstrappip module 2016-03-31 17:28:03 +02:00
coissac 4207db7c17 Transfers bug patch from orgasm 2016-03-31 16:53:09 +02:00
coissac 1cd35b3359 firt version of a fastq parser 2016-03-31 10:47:12 +02:00
coissac f51a6df5b2 Add a class buffering lines during a text file reading 2016-03-30 14:53:25 +02:00
coissac 94417e1330 patch the uncompress module to be able to deal with remote file 2016-03-29 20:57:39 +02:00
coissac 2e17dbce55 Adds a uopen function able to open transparently a local or a remote 
file compressed or not
 2016-03-29 20:56:54 +02:00
coissac a9eed1f5d9 Adds class for uncompressing transparently compressed files on line 2016-03-29 18:21:04 +02:00
coissac 2dfab3f378 Some changes in relation with the new obitools3.apps module 2016-03-28 15:05:59 +02:00
coissac e583098a96 change in the obi programme according to the new obitools3.apps module 
creation
 2016-03-28 15:05:02 +02:00
coissac b926ca3997 A template for a command 2016-03-28 15:04:06 +02:00
coissac aacfefad26 A set of utilitaty function for creating commands 2016-03-28 15:03:26 +02:00
coissac 2c084c8cf7 Switch to 10000000 per avl 2016-03-23 16:13:28 +01:00
coissac 6157633137 prototype for the obi unix command and the count sub command 2016-03-08 16:06:00 +01:00
coissac 0e50fbf706 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2015-09-03 08:38:57 -04:00
coissac f5937ec019 Deplacement des sources de la doc... 2015-09-02 04:50:50 -04:00
coissac a6395ebaf2 Transfert the distutil.ext from the org.asm project 2015-08-27 16:12:19 -04:00
coissac 32fd7b5a6b rename falsly named files *.pyx in *.pxd ;-) 2015-05-27 15:05:14 +02:00
coissac d1324618b8 Makes few cleanning and adds an obi_dms C constructor 2015-05-26 21:36:55 +02:00
coissac 9f69f76704 Few change on the obidms package 2015-05-26 14:17:08 +02:00
coissac 25da08f42c Patch few bugs in obidistutils 2015-05-26 14:15:06 +02:00
coissac 50c6040466 description of the obitools3 package for the python installer 2015-05-26 10:39:28 +02:00
coissac 6248160eeb C Syntax error patches 2015-05-26 10:38:56 +02:00
coissac 30ddb32dfe first skeleton of the obitools3 package 2015-05-26 10:38:15 +02:00
coissac 5948858a72 Patch few bugs in distutils.ext. 
This version seems able to install at list the empty package
 2015-05-25 16:55:09 +02:00
coissac fdfa51a8c7 A first version of the obidistutils adapted to Python3 2015-05-24 22:35:12 +02:00
coissac 809e5ad56a Patch the documentation 2015-05-23 16:51:56 +03:00
coissac 3aec0d7b50 Add function for estimating the size of an obitype or of an array of 
obitype.
 2015-05-23 16:50:49 +03:00
coissac 57db677d1f First minimal implementation of what should be the creation, opening and 
closing of an OBIDMS
 2015-05-23 16:29:06 +03:00
coissac 5e3e6f93c0 Add a mecanism similar to the classical errno system for reporting error 
but specific to the OBITools framwork
 2015-05-23 14:54:48 +03:00
coissac 3636672b2e Rename the two files to follow file naming conventions 2015-05-23 13:18:28 +03:00
coissac d5fcd52188 Add a function to test indianness of the platform 2015-05-23 11:39:00 +03:00
coissac 5138fe1db6 - Create a c-sandbox directory for experiences 
- Move the obicount tentative in the c-sandbox
 2015-05-23 10:41:14 +03:00
coissac db4603c2d7 change for the word collection in several places 2015-05-23 10:29:54 +03:00
coissac 41d8453e56 Merge branch 'master' of 
git@git.metabarcoding.org:obitools/obitools3.git

Conflicts:
	doc/source/formats.rst
	src/obicolumn.h
 2015-05-23 10:23:33 +03:00
coissac 76d714f10a Move UML image files in the UML directory 2015-05-23 09:55:44 +03:00
coissac a339905e73 restructuration of the documentation 2015-05-23 03:39:56 +03:00
coissac b0c9b295f1 An OBIDMS is also contitued by views 2015-05-12 14:54:10 +02:00
coissac 0b6c1f9f28 Add a .gitignore for the build directory in doc 2015-05-12 14:51:38 +02:00
coissac acea234d3a mv the doxyfile to the doc directory and change path to relative paths 2015-05-12 12:47:35 +02:00