9c9aec2556Cython API: the associated sequence column for a quality column can now be specified at the Python level
Celine Mercier
2018-08-08 19:49:56 +02:00
275d85dc5dCython: fixed a bug when reading an uncompressed file in binary mode where the first 4 characters would not be read
Celine Mercier
2018-07-28 17:11:51 +02:00
a39f9697beViews: added macro for taxid column name
Celine Mercier
2018-07-28 17:10:11 +02:00
b98880b7faVarious non-important fixes and comments
Celine Mercier
2018-07-28 17:07:17 +02:00
895d09b133obi import: 'taxid' columns are imported as 'TAXID' to fit view predicates, and fixed taxdump import and DMS closing
Celine Mercier
2018-07-28 17:03:00 +02:00
c02c15b93fCython API: URI decoding now returns the character string with the object path if it could not be opened
Celine Mercier
2018-07-28 17:00:42 +02:00
3e8c187f0bCython API: added EMBL parser and files to import are now read in binary mode
Celine Mercier
2018-07-28 16:57:01 +02:00
7f6d1597fcTaxonomy: added functions to check if a taxonomy already exists in a DMS, and added taxdump import from a compressed file
Celine Mercier
2018-07-28 16:48:11 +02:00
1de308a856obi clean: option to only keep heads now works, fixed a bug where last sequence was not properly labelled, and code is cleaned, fixed and error checked
Celine Mercier
2018-05-31 15:11:41 +02:00
892ed83a33Removed deprecated function declarations
Celine Mercier
2018-05-31 15:08:11 +02:00
6911bf4d70obi clean: first version
Celine Mercier
2018-05-18 14:26:54 +02:00
f0c147c252C API: Added a function to set an entire column to a specified (atomic) value.
Celine Mercier
2018-05-17 15:59:16 +02:00
4aef20add8Fixed a bug where the line selection column of a view would not be flagged as finished
Celine Mercier
2018-05-17 15:17:19 +02:00
62614a8538Cython API: fixed a bug in URI decoding and option handling where the quality offset would not be read properly
Celine Mercier
2018-05-17 15:10:52 +02:00
ffebc6acfbCython API: better handling of default quality offset value
Celine Mercier
2018-05-17 15:01:25 +02:00
b91b3176b0obi uniq: fixed a bug where merged values were wrongly reinitialized
Celine Mercier
2018-05-17 14:58:15 +02:00
31d8ba5085obi test: minor change
Celine Mercier
2018-05-17 14:54:45 +02:00
a166a169cfobi ngsfilter: fixed a bug with -u option
Celine Mercier
2018-05-17 14:53:53 +02:00
8a10072d99obi annotate: fixed a bug with --with-taxon-at-rank option and minor improvements
Celine Mercier
2018-05-17 14:51:18 +02:00
123fb9d7baCython API: in taxonomy, added get_taxon_at_rank() function for Taxonomy class and rank_idx property for Taxon class
Celine Mercier
2018-03-21 16:38:26 +01:00
4c3478d8f8Removed the predicate to check for a quality column (because for example with obi annotate, clone view so clone predicate, then modify seq, so quality is deleted, and predicate becomes a problem)
Celine Mercier
2018-03-21 16:37:19 +01:00
dad21823ffCython API: trying to guess the type of a column when adding a None value does not generate an exception anymore, and RollbackException can now rollback several views
Celine Mercier
2018-03-12 18:03:37 +01:00
96bf2daae8Cython API: added slices in Seq classes and fixes
Celine Mercier
2018-03-12 17:51:41 +01:00
e6c49b7941Cython API: moved an eval function to utils
Celine Mercier
2018-03-12 17:49:54 +01:00
4960662332Cython API: tobytes() function now handles None values
Celine Mercier
2018-03-12 17:25:12 +01:00
00993d4215Cython API: fixed a bug where the quality format would not be read properly from the configuration values
Celine Mercier
2018-02-12 14:42:30 +01:00
1a5b499b5cCython API to add an OBI_QUAL column after creating a view
Celine Mercier
2017-12-19 11:06:24 +01:00
b7b8ba7e5aBetter handling of elements names in Cython
Celine Mercier
2017-12-13 23:12:14 +01:00
e9e7fac999New obi uniq: stores columns with too many elements per line as character strings, and keeps a minimum of things in the memory
Celine Mercier
2017-12-13 22:49:08 +01:00
1fd3323372Columns: elements names informations are now kept in a memory arena of adapted size in the header, and added a boolean in the header indicating whether the values should be evaluated (typically character strings to be evaluated in Python)
Celine Mercier
2017-12-13 22:46:50 +01:00
2df5932b67Cython 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
Celine Mercier
2017-12-13 22:27:36 +01:00
b93b982a18Cython: added an option for input taxdump and and an option for the maximum number of elements in columns with multiple elements per line
Celine Mercier
2017-12-13 22:25:15 +01:00
ea73047fc7Added rewinddir before each readdir so that the directories are always read properly
Celine Mercier
2017-11-24 18:04:58 +01:00
0998268955Fixed two little potential bugs when cleaning unfinished columns and deleted old trace
Celine Mercier
2017-11-24 18:03:59 +01:00
31726407a3Taxonomy: fixed a bug where a pointer was not properly reallocated, and a bug where the merged list of taxids was not built correctly
Celine Mercier
2017-11-24 18:01:30 +01:00
d21f4a6f90Header parser: identifiers ending with ';' are now handled
Celine Mercier
2017-11-24 17:59:52 +01:00
9e3ac477ebOBIDMS: 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)
Celine Mercier
2017-11-24 17:58:47 +01:00
ee5d647d0dTaxonomy: fixed a bug un parental tree iterator
Celine Mercier
2017-11-24 17:55:17 +01:00
3ba7ce1c91View rollback: version files and column directories aren't deleted anymore to prevent indexer bug, and fixed a freeing bug
Celine Mercier
2017-11-15 17:27:26 +01:00
9a50803c00Added tuple columns containing immutable indexed data arrays of any type
Celine Mercier
2017-11-15 13:48:59 +01:00
1684f96b79Fixed a bug when flagging a read-only column as finished
Celine Mercier
2017-10-26 19:11:29 +02:00
43f65e7fd0obi uniq: fixed bug where dictionary indexes were not read properly, and added view rollback in case of an exception.
Celine Mercier
2017-10-26 19:00:05 +02:00
dfd51939a0Views are now rollbacked if an error occurs, and unfinished views and columns are deleted when an OBIDMS is opened.
Celine Mercier
2017-10-26 18:58:48 +02:00
1ae634d56bAdded atexit command to obi import, obi uniq and obi less
Celine Mercier
2017-10-16 11:09:55 +02:00
04e065094aAll DMS opened by a program are now listed and closed with atexit system
Celine Mercier
2017-10-16 10:35:07 +02:00
fb9b219abeFixed a bug with taxonomy URIs not being read correctly
Celine Mercier
2017-10-04 16:00:30 +02:00
09a5f89849Column API: improvements to be more flexible when referring to elements in columns with several elements per line.
Celine Mercier
2017-10-04 15:59:23 +02:00
535692b020Taxonomy: new functions and improvements
Celine Mercier
2017-10-04 15:55:13 +02:00
0ab081f79eUpdated obi test to work with changes in taxonomy API
Celine Mercier
2017-10-04 15:50:32 +02:00
1cb05de7e3Basic obi less
Celine Mercier
2017-10-04 15:46:26 +02:00
532d8e9cd7obi import: small efficiency improvement when dealing with NA values
Celine Mercier
2017-10-04 15:44:48 +02:00
ae24a807daobi uniq: added the option to merge ids, except it only works on small sets until lists are implemented properly using obiblobs
Celine Mercier
2017-09-25 17:28:03 +02:00
75c15594c4obi uniq: added option to use categories additionally to the sequence to determine uniqueness
Celine Mercier
2017-09-25 10:56:43 +02:00
5ed6835e0eFixed 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)
Celine Mercier
2017-09-25 10:52:19 +02:00
41dec03448Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
Celine Mercier
2017-09-18 16:08:31 +02:00
7c57bd33e5Added check to prevent views from having the name 'taxonomy' (used for URIs)
Celine Mercier
2017-09-15 14:54:55 +02:00
Celine Mercier
Eric Coissac