|
|
d21f4a6f90
|
Header parser: identifiers ending with ';' are now handled
|
2017-11-24 17:59:52 +01:00 |
|
|
|
9e3ac477eb
|
OBIDMS: Opened DMS now have a counter associated so that DMS are not
actually opened several times by the same program, which triggers the
cleaning of unfinished views and columns (to discuss)
|
2017-11-24 17:58:47 +01:00 |
|
|
|
ee5d647d0d
|
Taxonomy: fixed a bug un parental tree iterator
|
2017-11-24 17:55:17 +01:00 |
|
|
|
38fef5b9d4
|
obi test: better taxonomy testing
|
2017-11-24 17:54:10 +01:00 |
|
|
|
9a50803c00
|
Added tuple columns containing immutable indexed data arrays of any type
|
2017-11-15 13:48:59 +01:00 |
|
|
|
43f65e7fd0
|
obi uniq: fixed bug where dictionary indexes were not read properly, and
added view rollback in case of an exception.
|
2017-10-26 19:00:05 +02:00 |
|
|
|
dfd51939a0
|
Views are now rollbacked if an error occurs, and unfinished views and
columns are deleted when an OBIDMS is opened.
|
2017-10-26 18:58:48 +02:00 |
|
|
|
1ae634d56b
|
Added atexit command to obi import, obi uniq and obi less
|
2017-10-16 11:09:55 +02:00 |
|
|
|
04e065094a
|
All DMS opened by a program are now listed and closed with atexit system
|
2017-10-16 10:35:07 +02:00 |
|
|
|
5ddd1d9ae6
|
obi uniq: added taxonomy handling
|
2017-10-04 16:13:07 +02:00 |
|
|
|
f2ece573ff
|
Removed deprecated command
|
2017-10-04 16:09:41 +02:00 |
|
|
|
fb9b219abe
|
Fixed a bug with taxonomy URIs not being read correctly
|
2017-10-04 16:00:30 +02:00 |
|
|
|
09a5f89849
|
Column API: improvements to be more flexible when referring to elements
in columns with several elements per line.
|
2017-10-04 15:59:23 +02:00 |
|
|
|
535692b020
|
Taxonomy: new functions and improvements
|
2017-10-04 15:55:13 +02:00 |
|
|
|
0ab081f79e
|
Updated obi test to work with changes in taxonomy API
|
2017-10-04 15:50:32 +02:00 |
|
|
|
1cb05de7e3
|
Basic obi less
|
2017-10-04 15:46:26 +02:00 |
|
|
|
532d8e9cd7
|
obi import: small efficiency improvement when dealing with NA values
|
2017-10-04 15:44:48 +02:00 |
|
|
|
b4088a7928
|
Cython API: Added basic taxonomy option
|
2017-10-04 15:42:17 +02:00 |
|
|
|
ae24a807da
|
obi uniq: added the option to merge ids, except it only works on small
sets until lists are implemented properly using obiblobs
|
2017-09-25 17:28:03 +02:00 |
|
|
|
75c15594c4
|
obi uniq: added option to use categories additionally to the sequence to
determine uniqueness
|
2017-09-25 10:56:43 +02:00 |
|
|
|
41dec03448
|
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
|
2017-09-18 16:08:31 +02:00 |
|
|
|
a776e46e6d
|
Add the command name in the log
|
2017-09-15 14:51:13 +02:00 |
|
|
|
0e140df0fb
|
Cython API: added some imports in __init__ files
|
2017-09-14 18:30:04 +02:00 |
|
|
|
73bca6288f
|
New obi uniq
|
2017-08-20 18:04:21 +02:00 |
|
|
|
6a2759eee6
|
obi import with new input/ouput API
|
2017-08-20 17:58:36 +02:00 |
|
|
|
663a1a1091
|
Cython API: column elements: added possibility to check if an element
exists from its index, and a dict-like get() method
|
2017-08-20 17:44:05 +02:00 |
|
|
|
c6d5436a58
|
Cython API: fixed a bug where iteration on a NUC_SEQS view would not be
done correctly (bug appeared with optimization modifications done
lately)
|
2017-08-20 17:41:41 +02:00 |
|
|
|
47cad285d6
|
Cython API: fixed 2 little bugs in Seq API
|
2017-08-20 17:39:30 +02:00 |
|
|
|
74f15d1a23
|
Cython API: Various fixes in input handlers (parsers, openers etc).
Mostly working but not bug-free
|
2017-08-20 17:37:51 +02:00 |
|
|
|
7f1ff49aa2
|
Cython API to import a column and a view from a DMS to another DMS
|
2017-08-03 16:34:02 +02:00 |
|
|
|
407f61a408
|
Add the possibility to create temporary objects like a temporary
directory and a temporary DMS
|
2017-07-28 16:33:19 +02:00 |
|
|
|
35b0c55a8c
|
Cython API: various improvements and checks
|
2017-07-28 13:15:13 +02:00 |
|
|
|
b9c65a871f
|
Patch decoding of URL
|
2017-07-28 12:41:28 +02:00 |
|
|
|
84bb93096f
|
Cython API: fixes and improvements in Column API
|
2017-07-28 10:27:04 +02:00 |
|
|
|
01c69e7e25
|
Cython API: fixed a bug when printing a column
|
2017-07-28 10:01:56 +02:00 |
|
|
|
adf5cbef97
|
Added DMS method to create a DMS if it doesn't already exists, otherwise
opens it
|
2017-07-28 09:55:43 +02:00 |
|
|
|
da48a9d1af
|
Patch group of option : types must be callable not a string
|
2017-07-28 09:36:18 +02:00 |
|
|
|
9482c663c0
|
minor comments and changes
|
2017-07-27 19:46:34 +02:00 |
|
|
|
89e2f80fd8
|
Goes with previous commit
|
2017-07-27 19:43:00 +02:00 |
|
|
|
7112f44fb7
|
Bug fixes for input handlers, openers, parsers etc. Compiling but not
tested
|
2017-07-27 19:42:44 +02:00 |
|
|
|
b2fc1f4611
|
obi uniq: first version
|
2017-07-27 19:40:19 +02:00 |
|
|
|
75f691d55a
|
Cython API: Seq classes reworked
|
2017-07-27 19:39:58 +02:00 |
|
|
|
0655063bb0
|
Cython API: view_NUC_SEQS changes to go with previous commits
|
2017-07-27 19:39:26 +02:00 |
|
|
|
9701b1230c
|
Cython API: OBIWrapper.new method is now OBIWrapper.new_wrapper to avoid
mismatching method definitions with subclasses
|
2017-07-27 19:38:25 +02:00 |
|
|
|
f8a4428674
|
Cython API: DMS test_open method doesn't raise an exception anymore
|
2017-07-27 19:36:28 +02:00 |
|
|
|
1a0f18a11a
|
Cython API: added a __setitem__ method to the View class that can detect
if the item is a Line and create the corresponding columns if needed +
minor changes
|
2017-07-27 19:35:28 +02:00 |
|
|
|
3d7aa52c90
|
Cython API: Fixed a bug when setting NA values in Column_multi_elts, and
added some properties
|
2017-07-27 19:31:15 +02:00 |
|
|
|
69c50ff922
|
Cython API: added a Column subclass to allow direct access to indexes
for columns that store indexes referring to other data
|
2017-07-27 19:29:10 +02:00 |
|
|
|
c91969126b
|
Cython C API declarations to go with previous commit
|
2017-07-27 19:26:59 +02:00 |
|
|
|
15d383fa8b
|
Added possibility to specify the offset for encoding and decoding
sequence quality character strings
|
2017-07-27 19:24:41 +02:00 |
|
