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408 Commits 18 Branches 66 Tags
b5b889c4a28c0db3cdf27ab50bc1f568c4379a64
Commit Graph

192 Commits

Author SHA1 Message Date
Celine Mercier
9d042f7bd0 Refactored and relocated the set and get functions of all column types, 
both within and out of the context of a view
 2016-04-13 15:10:24 +02:00
Celine Mercier
5ec2d8842e Character string indexer API 2016-04-12 17:21:01 +02:00
Celine Mercier
be05c889e2 DNA_seq_indexer API 2016-04-12 16:38:47 +02:00
Celine Mercier
04e3a7b5a9 Added more references in cython .cfiles files because it seems necessary 
for linux distributions
 2016-04-12 15:10:54 +02:00
Celine Mercier
d8107533d8 Obiblob_indexer API 2016-04-12 14:53:33 +02:00
Eric Coissac
6fe4c6134a Allows for calling getConfiguration without parametter for geting the 
default configuration
 2016-04-11 13:31:09 +02:00
Celine Mercier
019dfc01b4 Branch to refactor and debug (AVLs bugged) 2016-04-08 15:38:57 +02:00
Eric Coissac
45c9c5075c A first version of the fasta parser 2016-04-01 18:15:54 +02:00
Eric Coissac
20b97c972b Add boolean type in the tag evaluation 2016-04-01 13:42:24 +02:00
Eric 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
Eric Coissac
1cd35b3359 firt version of a fastq parser 2016-03-31 10:47:12 +02:00
Eric Coissac
f51a6df5b2 Add a class buffering lines during a text file reading 2016-03-30 14:53:25 +02:00
Eric Coissac
94417e1330 patch the uncompress module to be able to deal with remote file 2016-03-29 20:57:39 +02:00
Eric 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
Eric Coissac
a9eed1f5d9 Adds class for uncompressing transparently compressed files on line 2016-03-29 18:21:04 +02:00
Eric Coissac
2dfab3f378 Some changes in relation with the new obitools3.apps module 2016-03-28 15:05:59 +02:00
Eric Coissac
e583098a96 change in the obi programme according to the new obitools3.apps module 
creation
 2016-03-28 15:05:02 +02:00
Eric Coissac
b926ca3997 A template for a command 2016-03-28 15:04:06 +02:00
Eric Coissac
aacfefad26 A set of utilitaty function for creating commands 2016-03-28 15:03:26 +02:00
Celine Mercier
ff6c27acf2 Implemented the retrieval of values with groups of AVLs 2016-03-25 15:35:16 +01:00
Celine Mercier
69856f18dd untested (and no possible retrieval) of CRC used to represent data in 
AVL trees
 2016-03-24 16:38:11 +01:00
Celine Mercier
d44117d625 obiimport function for testing purposes 2016-03-23 13:00:02 +01:00
Celine Mercier
4085904362 Merge branch 'multiple_avls_bloom' 2016-03-22 14:14:10 +01:00
Celine Mercier
383e738ab7 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-03-18 15:49:53 +01:00
Celine Mercier
3681cecb4d Multiple AVLs with bloom filters (very raw test version) 2016-03-18 11:06:02 +01:00
Celine Mercier
21d1b2ed3e First implementation of taxonomy reading 2016-03-11 13:56:38 +01:00
Eric Coissac
6157633137 prototype for the obi unix command and the count sub command 2016-03-08 16:06:00 +01:00
Celine Mercier
a08def47e6 It is now impossible to create a view with a name identical to one of an 
existing written view
 2016-03-01 13:36:54 +01:00
Celine Mercier
fc5a12bad7 Closes #34 2016-02-29 17:56:55 +01:00
Celine Mercier
e323d8e702 Cython classes for nucleotide sequences (outside or in the context of a 
view)
 2016-02-29 16:33:30 +01:00
Celine Mercier
4df313c54a Added Obiviews specialized for the handling of nucleotide sequences 2016-02-25 09:43:27 +01:00
Celine Mercier
ffc68d448f Deleted a forgotten print statement 2016-02-18 15:15:42 +01:00
Celine Mercier
a8f03248a8 Major update : views 2016-02-18 10:38:51 +01:00
Celine Mercier
c139367555 DNA sequences and character strings are now handled using AVL trees. 2015-12-11 17:24:44 +01:00
Celine Mercier
1586956d57 Added the lists of opened columns and arrays in the OBIDMS structure, 
and a counter in the OBIDMS column structure; fixed some bugs and
created tests for referring columns that are bound to disappear anyway.
 2015-12-02 17:32:07 +01:00
Celine Mercier
b45b496b0e Major update: new type of columns containing indices referring to lines 
in other columns
 2015-11-29 11:57:07 +01:00
Celine Mercier
2cf10cb6f0 Column type is now passed as a character string when creating the column 
(either 'OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_STR' or
'OBI_SEQ')
 2015-11-23 15:48:27 +01:00
Celine Mercier
5a5516303d deleting useless .pyc files 2015-11-23 14:43:34 +01:00
Celine Mercier
6aa2f92930 DNA sequences are now encoded on 4 bits when they are in IUPAC 2015-11-20 15:32:09 +01:00
Celine Mercier
6ab1c83302 New column type for DNA sequences. Only for those coded on 2 bits (only 
'ATGCatgc') for now.
 2015-11-19 18:12:48 +01:00
Celine Mercier
e371248567 changed version to 0.0.0 2015-11-19 18:11:21 +01:00
Celine Mercier
e8417b4f6f The endianness of an OBIDMS is now stored in an informations file that 
is read when opening the OBIDMS.
 2015-11-16 14:37:51 +01:00
Celine Mercier
6579566c6e Minor changes in code to improve readability and fix C compilation 
warnings
 2015-11-10 14:37:58 +01:00
Celine Mercier
410e2e02a0 When retrieving the header of a column, the version number of the column 
wanted can now be provided.
 2015-11-10 13:30:10 +01:00
Celine Mercier
661fe3606a In OBI_CHAR columns, characters are now given and retrieved as decoded 
(unicode) characters.
 2015-11-10 11:24:08 +01:00
Celine Mercier
c4b7e579cf Comments in column headers are now working. 2015-11-10 10:56:45 +01:00
Celine Mercier
0e3d6ed2d7 Methods __len__ (number of lines used) and __sizeof__ (total size in 
bytes) implemented for columns.
 2015-11-09 15:56:20 +01:00
Celine Mercier
9b066f4327 Major update: obiarrays with columns containing indices referring to 
character strings.
 2015-11-06 17:55:15 +01:00
Celine Mercier
456551ffeb obi arrays that don't work because of cython bug passing wrong pointers 2015-11-03 14:22:00 +01:00
Celine Mercier
ecb9d97adb Reorganized the code to have less functions, and the functions to get 
and format the creation date of a column are now working.
 2015-10-15 15:12:45 +02:00