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abandoned_branch_for_column_comparison_functions
Commit Graph

117 Commits

Author SHA1 Message Date
Celine Mercier
1a2d552567 Abandoned beginning of functions to apply comparisons to whole columns 
(not worth it for now as comparisons are already fast enough)
 2016-05-04 13:39:55 +02:00
Celine Mercier
bc12360490 Reworked and commented a bit the cython layer for dms, columns and views 2016-05-02 15:16:06 +02:00
Celine Mercier
872071b104 Removed a list of column pointers kept in the OBIView class that was not 
really needed
 2016-05-02 14:23:42 +02:00
Celine Mercier
baba2d742e commenting _obidms.pyx 2016-04-29 16:07:03 +02:00
Celine Mercier
0eca86107e Pseudo obihead for tests 2016-04-27 14:27:28 +02:00
Celine Mercier
0de953a3ef pseudo obigrep for tests 2016-04-27 14:19:55 +02:00
Celine Mercier
d159b921eb Fixed obi import trying to print all lines at the end (source of 
segfault?)
 2016-04-27 13:14:19 +02:00
Celine Mercier
4e4cf46b16 Added all C files as source files for all cython files to stop having 
that kind of problem with linux systems
 2016-04-27 10:44:24 +02:00
Celine Mercier
6b61533650 Added more C source files for _obiseq 2016-04-27 10:41:00 +02:00
Celine Mercier
419885485b Added files in _obitaxo C sources for cython 2016-04-27 10:30:16 +02:00
Celine Mercier
a6c8d35491 import command a bit modified for tests 2016-04-26 14:29:54 +02:00
Celine Mercier
366264828e Renamed MurmurHash2.c file to murmurhash2.c as it could be a problem 2016-04-26 14:29:17 +02:00
Celine Mercier
87935c6678 Fixed all compilation problems with new function names, locations etc 2016-04-25 18:35:02 +02:00
Celine Mercier
92980508c0 Made the function to clone a column in the context of a view private 2016-04-25 18:15:25 +02:00
Celine Mercier
1fbbdd43f9 Updated obiversion_t declaration 2016-04-25 17:58:37 +02:00
Celine Mercier
8cdfbb379e Documentation for views and reworked the code a little 2016-04-25 17:58:12 +02:00
Celine Mercier
7a88ca619a First obi import (doesn't import tags yet because NA values aren't 
handled)
 2016-04-15 17:00:08 +02:00
Celine Mercier
eddd19a245 Changes in obi commands 2016-04-15 16:59:21 +02:00
Celine Mercier
2aafecc3b5 Changed sequence 'description' to 'definition' everywhere 2016-04-15 16:31:43 +02:00
Celine Mercier
094b2371e9 Deleted obsolete directory 2016-04-15 14:44:31 +02:00
Celine Mercier
c1034d300d merging and fixed git conflict with obiavl.h 2016-04-15 13:23:29 +02:00
Celine Mercier
02d67c257f The default name of an AVL is now the column name + '_indexer', and when 
an AVL is opened (as opposed to created), it is read-only
 2016-04-15 12:55:26 +02:00
Celine Mercier
e04ea85d1e Fixed problematic __str__ method and useless declarations in the 
OBI_Nuc_Seq_Stored class
 2016-04-15 11:22:05 +02:00
Celine Mercier
73d64e5aff Renamed 'unmap_header' function to 'close_header' 2016-04-14 15:19:27 +02:00
Celine Mercier
4cb52e1632 Made the truncating of columns automatic when closing them (note: 
already the case for AVLs)
 2016-04-14 15:13:30 +02:00
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