|
|
2df5932b67
|
Cython column API: fixed a memory leak, optimized the reading of
elements names, added a __len__ method to Column_line, and the API for
columns with character strings to evaluate
|
2017-12-13 22:27:36 +01:00 |
|
|
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b93b982a18
|
Cython: added an option for input taxdump and and an option for the
maximum number of elements in columns with multiple elements per line
|
2017-12-13 22:25:15 +01:00 |
|
|
|
ea73047fc7
|
Added rewinddir before each readdir so that the directories are always
read properly
|
2017-11-24 18:04:58 +01:00 |
|
|
|
0998268955
|
Fixed two little potential bugs when cleaning unfinished columns and
deleted old trace
|
2017-11-24 18:03:59 +01:00 |
|
|
|
31726407a3
|
Taxonomy: fixed a bug where a pointer was not properly reallocated, and
a bug where the merged list of taxids was not built correctly
|
2017-11-24 18:01:30 +01:00 |
|
|
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d21f4a6f90
|
Header parser: identifiers ending with ';' are now handled
|
2017-11-24 17:59:52 +01:00 |
|
|
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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 |
|
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|
ee5d647d0d
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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 |
|
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3ba7ce1c91
|
View rollback: version files and column directories aren't deleted
anymore to prevent indexer bug, and fixed a freeing bug
|
2017-11-15 17:27:26 +01:00 |
|
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9a50803c00
|
Added tuple columns containing immutable indexed data arrays of any type
|
2017-11-15 13:48:59 +01:00 |
|
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|
1684f96b79
|
Fixed a bug when flagging a read-only column as finished
|
2017-10-26 19:11:29 +02:00 |
|
|
|
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 |
|
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|
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 |
|
|
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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 |
|
|
|
9fc6868341
|
Increased maximum length for elements names
|
2017-10-04 16:10:53 +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 |
|
|
|
5ed6835e0e
|
Fixed a bug where the new line count when truncating a column would not
be computed correctly when dealing with high numbers (bad automatic type
for intermediate result)
|
2017-09-25 10:52:19 +02:00 |
|
|
|
41dec03448
|
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
|
2017-09-18 16:08:31 +02:00 |
|
|
|
7c57bd33e5
|
Added check to prevent views from having the name 'taxonomy' (used for
URIs)
|
2017-09-15 14:54:55 +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 |
|
|
|
4bb071c048
|
Merge branch 'master' of
git@git.metabarcoding.org:obitools/obitools3.git
Conflicts:
python/obitools3/commands/import.pyx
|
2017-09-05 08:59:45 +02:00 |
|
|
|
5045d0c2e9
|
xxx
|
2017-09-05 08:58:07 +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 |
|
|
|
38029b1f77
|
Forgot a ;
|
2017-08-20 17:56:18 +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 |
|
|
|
c559ddf487
|
BUG FIX: creation of a new column would fail because of a case not
handled when a high number of elements per line would imply less than
one line per memory page
|
2017-08-20 17:30:23 +02:00 |
|
|
|
93cff94e7f
|
Fixed some compilation warnings
|
2017-08-20 17:25:58 +02:00 |
|
|
|
9744a48a67
|
BUG FIX: seemingly identical obiblobs would have different hash values
because of the padding added by the compiler. Fixed by using calloc
instead of malloc for obiblob memory allocation.
|
2017-08-20 17:25:15 +02:00 |
|
|
|
6afdc9fb5f
|
AVLs: Added an error check
|
2017-08-20 17:21:06 +02:00 |
|
|
|
6f202363f4
|
Fixed a typo in doc
|
2017-08-20 17:20:13 +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 |
|
|
|
4b86aa67a8
|
New C functions to import a column and a view from a DMS to another DMS
|
2017-08-03 16:33:12 +02:00 |
|
|
|
a3e81930c2
|
Views: finished handling and documenting the conditions for an existing
column to be added to a view
|
2017-08-03 16:32:22 +02:00 |
|
