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Author SHA1 Message Date
Celine Mercier 15e43bb9a1 Cython API: obi import can now import ngsfilter files and tabular files 2018-03-12 18:10:43 +01:00
Celine Mercier 8a0b95c1d6 New command: obi ngsfilter 2018-03-12 18:09:22 +01:00
Celine Mercier dd225a255f obi uniq: better error checking 2018-03-12 18:04:53 +01:00
Celine Mercier dad21823ff Cython 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
 2018-03-12 18:03:37 +01:00
Celine Mercier 96bf2daae8 Cython API: added slices in Seq classes and fixes 2018-03-12 17:51:41 +01:00
Celine Mercier e6c49b7941 Cython API: moved an eval function to utils 2018-03-12 17:49:54 +01:00
Celine Mercier 4960662332 Cython API: tobytes() function now handles None values 2018-03-12 17:25:12 +01:00
Celine Mercier b2cfa4b52f Cython Sequence classes: reworked improved etc 2018-02-12 14:54:47 +01:00
Celine Mercier 94a899de12 Cython View API: added small tools 2018-02-12 14:48:27 +01:00
Celine Mercier b48330a5c9 Fixed a little bug when cleaning unfinished views 2018-02-12 14:44:56 +01:00
Celine Mercier 74d880b817 Fixed default quality offset 2018-02-12 14:43:44 +01:00
Celine Mercier 00993d4215 Cython API: fixed a bug where the quality format would not be read 
properly from the configuration values
 2018-02-12 14:42:30 +01:00
Celine Mercier 370fb9272c obi uniq: better typing 2018-02-12 14:38:07 +01:00
Celine Mercier c8097e14e1 obi import: removed old traces 2018-02-12 14:36:56 +01:00
Celine Mercier 01ef85658c New command: obi alignpairedend 2018-02-12 13:30:06 +01:00
Celine Mercier f5a00c9322 Cython alignment library 2018-02-12 13:28:20 +01:00
Celine Mercier 156fb04e88 Implemented functions to build reverse complement sequences 2018-01-05 16:08:36 +01:00
Celine Mercier 428c4eb5e6 obi import: fixed creation of quality columns (to discuss) 2017-12-19 11:07:00 +01:00
Celine Mercier 1a5b499b5c Cython API to add an OBI_QUAL column after creating a view 2017-12-19 11:06:24 +01:00
Celine Mercier b7b8ba7e5a Better handling of elements names in Cython 2017-12-13 23:12:14 +01:00
Celine Mercier e9e7fac999 New obi uniq: stores columns with too many elements per line as 
character strings, and keeps a minimum of things in the memory
 2017-12-13 22:49:08 +01:00
Celine Mercier 1fd3323372 Columns: 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)
 2017-12-13 22:46:50 +01:00
Celine Mercier 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
Celine Mercier 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
Celine Mercier ea73047fc7 Added rewinddir before each readdir so that the directories are always 
read properly
 2017-11-24 18:04:58 +01:00
Celine Mercier 0998268955 Fixed two little potential bugs when cleaning unfinished columns and 
deleted old trace
 2017-11-24 18:03:59 +01:00
Celine Mercier 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
Celine Mercier d21f4a6f90 Header parser: identifiers ending with ';' are now handled 2017-11-24 17:59:52 +01:00
Celine Mercier 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
Celine Mercier ee5d647d0d Taxonomy: fixed a bug un parental tree iterator 2017-11-24 17:55:17 +01:00
Celine Mercier 38fef5b9d4 obi test: better taxonomy testing 2017-11-24 17:54:10 +01:00
Celine Mercier 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
Celine Mercier 9a50803c00 Added tuple columns containing immutable indexed data arrays of any type 2017-11-15 13:48:59 +01:00
Celine Mercier 1684f96b79 Fixed a bug when flagging a read-only column as finished 2017-10-26 19:11:29 +02:00
Celine Mercier 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
Celine Mercier 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
Celine Mercier 1ae634d56b Added atexit command to obi import, obi uniq and obi less 2017-10-16 11:09:55 +02:00
Celine Mercier 04e065094a All DMS opened by a program are now listed and closed with atexit system 2017-10-16 10:35:07 +02:00
Celine Mercier 5ddd1d9ae6 obi uniq: added taxonomy handling 2017-10-04 16:13:07 +02:00
Celine Mercier 9fc6868341 Increased maximum length for elements names 2017-10-04 16:10:53 +02:00
Celine Mercier f2ece573ff Removed deprecated command 2017-10-04 16:09:41 +02:00
Celine Mercier fb9b219abe Fixed a bug with taxonomy URIs not being read correctly 2017-10-04 16:00:30 +02:00
Celine Mercier 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
Celine Mercier 535692b020 Taxonomy: new functions and improvements 2017-10-04 15:55:13 +02:00
Celine Mercier 0ab081f79e Updated obi test to work with changes in taxonomy API 2017-10-04 15:50:32 +02:00
Celine Mercier 1cb05de7e3 Basic obi less 2017-10-04 15:46:26 +02:00
Celine Mercier 532d8e9cd7 obi import: small efficiency improvement when dealing with NA values 2017-10-04 15:44:48 +02:00
Celine Mercier b4088a7928 Cython API: Added basic taxonomy option 2017-10-04 15:42:17 +02:00
Celine Mercier 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
Celine Mercier 75c15594c4 obi uniq: added option to use categories additionally to the sequence to 
determine uniqueness
 2017-09-25 10:56:43 +02:00
Celine Mercier 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
Celine Mercier 41dec03448 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2017-09-18 16:08:31 +02:00
Celine Mercier 7c57bd33e5 Added check to prevent views from having the name 'taxonomy' (used for 
URIs)
 2017-09-15 14:54:55 +02:00
Celine Mercier 0e140df0fb Cython API: added some imports in __init__ files 2017-09-14 18:30:04 +02:00
Celine Mercier 73bca6288f New obi uniq 2017-08-20 18:04:21 +02:00
Celine Mercier 6a2759eee6 obi import with new input/ouput API 2017-08-20 17:58:36 +02:00
Celine Mercier 38029b1f77 Forgot a ; 2017-08-20 17:56:18 +02:00
Celine Mercier 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
Celine Mercier 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
Celine Mercier 47cad285d6 Cython API: fixed 2 little bugs in Seq API 2017-08-20 17:39:30 +02:00
Celine Mercier 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
Celine Mercier 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
Celine Mercier 93cff94e7f Fixed some compilation warnings 2017-08-20 17:25:58 +02:00
Celine Mercier 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
Celine Mercier 6afdc9fb5f AVLs: Added an error check 2017-08-20 17:21:06 +02:00
Celine Mercier 6f202363f4 Fixed a typo in doc 2017-08-20 17:20:13 +02:00
Celine Mercier 7f1ff49aa2 Cython API to import a column and a view from a DMS to another DMS 2017-08-03 16:34:02 +02:00
Celine Mercier 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
Celine Mercier 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
Celine Mercier 644b55b49f Fixed doc typo 2017-08-03 16:29:25 +02:00
Celine Mercier 927c684fc2 Utils: new function to copy the content of a file into another file 2017-08-03 16:28:54 +02:00
Celine Mercier 344566d9e9 AVLs: made some functions public and changed some rights to be able to 
import AVLs from a DMS to another
 2017-08-03 16:27:43 +02:00
Celine Mercier 35b0c55a8c Cython API: various improvements and checks 2017-07-28 13:15:13 +02:00
Celine Mercier 84bb93096f Cython API: fixes and improvements in Column API 2017-07-28 10:27:04 +02:00
Celine Mercier 01c69e7e25 Cython API: fixed a bug when printing a column 2017-07-28 10:01:56 +02:00
Celine Mercier 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
Celine Mercier 9482c663c0 minor comments and changes 2017-07-27 19:46:34 +02:00
Celine Mercier c5f3fdc295 Increased maximum element names length in columns 2017-07-27 19:44:49 +02:00
Celine Mercier 89e2f80fd8 Goes with previous commit 2017-07-27 19:43:00 +02:00
Celine Mercier 7112f44fb7 Bug fixes for input handlers, openers, parsers etc. Compiling but not 
tested
 2017-07-27 19:42:44 +02:00
Celine Mercier b2fc1f4611 obi uniq: first version 2017-07-27 19:40:19 +02:00
Celine Mercier 75f691d55a Cython API: Seq classes reworked 2017-07-27 19:39:58 +02:00
Celine Mercier 0655063bb0 Cython API: view_NUC_SEQS changes to go with previous commits 2017-07-27 19:39:26 +02:00
Celine Mercier 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
Celine Mercier f8a4428674 Cython API: DMS test_open method doesn't raise an exception anymore 2017-07-27 19:36:28 +02:00
Celine Mercier 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
Celine Mercier 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
Celine Mercier 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
Celine Mercier c91969126b Cython C API declarations to go with previous commit 2017-07-27 19:26:59 +02:00
Celine Mercier 15d383fa8b Added possibility to specify the offset for encoding and decoding 
sequence quality character strings
 2017-07-27 19:24:41 +02:00
Celine Mercier 99ceed5fff Cython API: renamed OBI_Taxonomy to Taxonomy and OBI_Taxon to Taxon 2017-07-27 19:21:45 +02:00
Celine Mercier 59dd0a8a8c Standardized and improved the API to create new columns, updated the doc 2017-07-18 17:34:32 +02:00
Celine Mercier c88df2e12c First version of automatic ID and COUNT columns, to discuss (for now, 
columns created when NUC_SEQ views are closed if the columns don't
already exist)
 2017-07-17 17:31:09 +02:00
Celine Mercier 1e57bfacb4 Fixed some C documentation 2017-07-17 16:45:08 +02:00
Celine Mercier 3e6aecc635 Added a C function to add a COUNT column to a view with all lines set to 
1
 2017-07-11 16:44:23 +02:00
Celine Mercier ced9a268a1 obi import: added an option to specify the NA value in the input file 
(default is 'NA', same as in R's read.table function)
 2017-07-11 12:10:33 +02:00
Celine Mercier df2ad41150 Cython APi: Added a width property to views, corresponding to their 
column count
 2017-07-11 11:46:32 +02:00
Celine Mercier f8895e879d Cython API: Added a function to get a column from its index in the view 2017-07-11 11:36:42 +02:00
Celine Mercier b729b8928f obi less: fixed bug when the length of a view would be less than the 
default number of lines printed
 2017-07-10 17:04:02 +02:00
Celine Mercier b6b95f26b6 obi import: Skipping sequences is now done through the iterators so that 
sequences are not uselessly parsed
 2017-07-10 17:02:30 +02:00