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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 04c9470f7d Fixed and cleaned DNA_seq_indexer API 2016-04-12 17:20:24 +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
Celine Mercier cd4e65e190 Fixed typo and includes in obiblob files 2016-04-12 14:52:27 +02:00
Celine Mercier 375bfcce8a Renamed "Obi_byte_arrays" to "Obiblobs" and moved Obiblob functions to 
separate obiblob.c and obiblob.h files
 2016-04-12 11:21:14 +02:00
Celine Mercier c225cfd8b6 Fixed bug with retrieval of values from AVLs (bad cast in byte array 
structure)
 2016-04-11 17:07:22 +02:00
coissac 6fe4c6134a Allows for calling getConfiguration without parametter for geting the 
default configuration
 2016-04-11 13:31:09 +02:00
Celine Mercier 966b1325ed Deleted declaration of obsolete public function 2016-04-11 11:14:20 +02:00
Celine Mercier 019dfc01b4 Branch to refactor and debug (AVLs bugged) 2016-04-08 15:38:57 +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
Celine Mercier edc4fd7b3e Fixed minor warning 2016-03-25 16:11:52 +01:00
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
coissac 2c084c8cf7 Switch to 10000000 per avl 2016-03-23 16:13:28 +01:00
Celine Mercier 58ac860cc7 Added macro for the bloom filter parameters and deleted old unused 
macros for crc
 2016-03-23 13:33:40 +01:00
Celine Mercier d44117d625 obiimport function for testing purposes 2016-03-23 13:00:02 +01:00
Celine Mercier 6bd42132c4 Minor fixes to silence warnings and replaced two asprintf uses 2016-03-23 12:58:53 +01:00
Celine Mercier 4085904362 Merge branch 'multiple_avls_bloom' 2016-03-22 14:14:10 +01:00
Celine Mercier b04b4b5902 made POSIX compliant 2016-03-21 11:33:06 +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 545ed8111a Code for tests storing data in multiple AVLs. 
(note: unretrievable data as implemented)
 2016-03-11 15:34:55 +01:00
Celine Mercier 86071d30c9 Minor improvement in AVL initial size calculation 2016-03-11 14:07:40 +01:00
Celine Mercier 21d1b2ed3e First implementation of taxonomy reading 2016-03-11 13:56:38 +01:00
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 b350ea0393 Fixed minor error 2016-02-29 16:28:34 +01:00
Celine Mercier 8e9e21a02e Increased the maximum depth of AVL trees 2016-02-29 16:27:23 +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 cfaf069095 Fixed more typos and formatting imperfections. 2015-12-11 17:37:25 +01:00