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Author SHA1 Message Date
coissac da48a9d1af Patch group of option : types must be callable not a string 2017-07-28 09:36:18 +02:00
coissac fa8f826cdc Cleanup the end of the file 2017-07-27 16:07:39 +02:00
coissac dc91174a5e Complete the input option group functions 2017-07-27 16:06:48 +02:00
coissac ec65f00cf2 Complete the fasta iterator to manage new input options 2017-07-27 16:05:30 +02:00
coissac 8d9cdb4d03 Complete the fastq iterator to manage new input options 2017-07-27 16:05:17 +02:00
coissac 949e5f9baf Make a first full version of the URI decoder 2017-07-27 16:04:31 +02:00
coissac 3c6a05be54 Add option to the default config corresponding to the parsing of the 
inputs
 2017-07-27 16:03:47 +02:00
coissac 8781ecab1f Add a factory checking the file format and returning the correct 
iterator. First version working only with fasta and fastq nucleic
formats
 2017-07-27 16:02:52 +02:00
coissac 0f6ae7dfa6 Options stuff... ;-) 2017-07-25 13:07:03 +02:00
coissac 28259cd88b Beginning of URI decoder -- !!! NOT YET FULLY IMPLEMENTED !!! 2017-07-25 13:05:58 +02:00
coissac b24be84b0a Add a first group of options 2017-07-25 11:14:30 +02:00
coissac 6dccaa0213 Patch the registering function : register_all_column_classes 2017-04-06 15:37:51 +02:00
coissac cf7f2de016 Modify __init__ and close method to deal with registration process 2017-01-10 14:26:16 +01:00
coissac 5122ad52a7 Merge branch 'Eric_new_Python_API' of git@git.metabarcoding.org:obitools/obitools3.git into Eric_new_Python_API 2017-01-10 14:07:50 +01:00
coissac 4b02ba73ac Add the OBIObject concept 2017-01-10 14:07:10 +01:00
coissac 4a1d3167a7 Last change on my branch 2017-01-02 16:46:52 +01:00
coissac 153c22257f Last change on my branch 2017-01-02 16:46:17 +01:00
coissac 2139bfc748 refactoring... 2017-01-02 13:05:22 +01:00
coissac 65f3b16e6d Refactoring ... 2016-12-29 18:22:05 +01:00
coissac 0526386337 first working DMS class 2016-12-27 06:17:45 +01:00
coissac 62caf1346e temporary remove some files 2016-12-26 15:03:24 +01:00
coissac 3ac6e85fb3 Big refactoring 4 2016-12-26 14:58:03 +01:00
coissac 5156f6bb9e Big refactoring 3 2016-12-26 14:18:01 +01:00
coissac e6db2086d5 Big refactoring 2 2016-12-26 13:56:31 +01:00
coissac daacd0df76 Strong refactoring 1 2016-12-26 13:35:31 +01:00
coissac 3cedd00d7f Add register function for column type 2016-12-20 11:13:57 +01:00
coissac 82fbe43980 transfert method to obiviews 2016-12-20 08:18:47 +01:00
coissac d1a972dfcb patch import 2016-12-20 08:15:42 +01:00
coissac f43dc3e3ab separate the obicolumn classes in new files 2016-12-20 08:15:08 +01:00
coissac 04d39c62ab Try for a new API 2016-12-14 08:44:44 +01:00
coissac 06cb7a9a58 Some change in the way to manage access to special items of the 
dictionary like sequence or quality
 2016-12-13 12:49:34 +01:00
coissac fc55fc117d Some cosmetic on the code 2016-12-13 12:48:13 +01:00
coissac 4ef5cb0d87 Move the OBIView_NUC_SEQS class to files _obiview_nuc_seq.pxd and 
_obiview_nuc_seq.pyx to avoid circular inclusion
 2016-12-13 12:46:49 +01:00
coissac fc805e5443 Remove some warnings in the editor 2016-12-13 08:29:22 +01:00
coissac 8d7ef7d3d1 patch the distutils to add the C source directory in the include path. 
This should solve most of the compilation problems related to .h files
located in this directory
 2016-12-13 08:02:09 +01:00
coissac 6adb9eb623 Should solde issue #56 2016-09-19 21:40:40 +02:00
coissac 400a3f9f3d Merge branch 'Eric_version_for_sequence' 
Conflicts:
	python/obitools3/obidms/_obidmscolumn_seq.pyx
 2016-08-04 09:42:42 +02:00
coissac d1d26b9028 Simplify the code 2016-08-04 08:00:54 +02:00
coissac 465ea81c77 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-08-03 10:13:47 +02:00
coissac 1e6d6e32e0 Switch to Cython version >= 0.24 2016-08-03 10:13:10 +02:00
coissac ccc877764e Patch a bug in the printing of the progress bar leading to a bus error 
when compiled with some C compilers and Cython >= 0.24
 2016-08-03 10:12:23 +02:00
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