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5c50e5b378a3240ce8ea07ef1fa2d4fce80eea79
Commit Graph

209 Commits

Author SHA1 Message Date
Celine Mercier
5c50e5b378 Embryo of code for openMP parallelization of LCS alignment but 
deactivated for now because can't make it compile with cython/clang
 2016-12-20 11:46:58 +01:00
Celine Mercier
9c71b06117 Removed deprecated TODOs 2016-12-19 14:36:40 +01:00
Celine Mercier
3bf5260174 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-12-19 10:31:18 +01:00
Celine Mercier
857a5198e4 Updated `obi lcs` for the LCS alignment of two columns 2016-12-16 19:40:36 +01:00
Celine Mercier
490f5fe6b9 Updated deprecated code in cython API for columns (using line count of 
view instead of column)
 2016-12-16 19:04:21 +01:00
Celine Mercier
191c83aafc Added missing *.cfiles 2016-12-15 15:28:34 +01:00
Eric Coissac
fc805e5443 Remove some warnings in the editor 2016-12-13 08:29:22 +01:00
Celine Mercier
8afb1644e9 Alignment: API rework. 'obi align' is now 'obi lcs', and the results are 
now written to columns automatically created in the output view, all
optimally handled at the C level.
 2016-12-12 11:58:59 +01:00
Celine Mercier
fa4e4ffaff Changed the cython API to create new views so as to have different 
functions for the different cases
 2016-12-07 14:17:57 +01:00
Celine Mercier
936be64c34 Goes with 5e0c9f87 (missing ';' and fixed compilation warnings) 2016-12-05 11:18:29 +01:00
Celine Mercier
852e5488c8 The default element names for columns with multiple elements per line 
are now "O;1;2;...;n"
 2016-12-02 17:54:51 +01:00
Celine Mercier
98d0849653 Sequence alignment: added the possibility to specify the index of the 
sequences to align in a column containing multiple sequences per line (C
level for now)
 2016-11-29 16:15:02 +01:00
Celine Mercier
76a4c6b14e Fixed a bug when cloning a view and checking its type 2016-11-23 11:28:17 +01:00
Celine Mercier
70c49e214a Added the kmer filter to LCS alignments, and now obiblobs containing 
encoded sequences are directly put in int16_t arrays for the alignment
 2016-11-18 16:29:28 +01:00
Celine Mercier
1c71c195fc Goes with a0ebc2d8 2016-11-10 15:01:29 +01:00
Celine Mercier
359578814b Added view type property to OBIView cython class and updated obi export 
to use it
 2016-11-08 17:49:59 +01:00
Celine Mercier
51b23915ca Added properties for Nuc_Seq cython classes (and updated commands using 
them)
 2016-11-08 16:59:32 +01:00
Celine Mercier
b5b889c4a2 Fixed the OBI_Nuc_Seq_Stored cython class not being up to date with the 
new properties of its parent class
 2016-11-08 11:26:37 +01:00
Celine Mercier
36ac315125 Fixed bugs with python view type when creating a new view, and a bug 
when trying to guess the obi type of a nucleotide sequence when its type
was bytes
 2016-11-08 11:23:54 +01:00
Celine Mercier
8291693309 obi grep: updated to work with the new line selection class and within 
the local sequence environment, and progress bar functioning
 2016-11-08 11:19:12 +01:00
Celine Mercier
4bc19c3e49 obi export: view type is now checked and progress bar functioning 2016-11-08 11:17:20 +01:00
Celine Mercier
2d2fe5279d Added functions to add new taxa to a taxonomy with handling of 
associated *.ldx files
 2016-11-03 17:59:21 +01:00
Celine Mercier
2504bf0fa9 Added an iterator to the OBI_Taxonomy cython class 2016-11-02 11:08:18 +01:00
Celine Mercier
d8a257e711 Taxonomy handling functions in C. Features: read taxdump, read binary 
files, write binary files. Not fully handled yet: *.adx, *.pdx, *.ldx,
merged.dmp and delnodes.dmp files.
 2016-10-27 18:56:11 +02:00
Celine Mercier
b63d0fb9fb Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a 
taxonomy C structure
 2016-10-14 17:03:10 +02:00
Celine Mercier
1b07109e51 Removed deprecated code 2016-10-10 17:01:51 +02:00
Celine Mercier
60ab503a14 Added properties in the OBI_Taxonomy class 2016-10-10 17:01:17 +02:00
Celine Mercier
2dcfdc59fc When a new view is created with a line selection, the view to clone is 
automatically found + compacted redundant code + fixed potential bug
when cloning a NUC_SEQS view by name
 2016-10-06 17:55:18 +02:00
Celine Mercier
399fc2c051 Removed deprecated source files previously used for tests 2016-09-30 17:49:37 +02:00
Celine Mercier
9cd57deca9 Added OBIView_line_selection class to make new line selections 
associated with the view to clone, and improved and renamed method
closing a view
 2016-09-30 17:48:53 +02:00
Celine Mercier
d88811ed7d Added a seed option to the obi test command for reproducible tests 2016-09-29 17:34:48 +02:00
Celine Mercier
8c402101e4 Renamed private attributes as _* and removed some deprecated code 2016-09-28 16:56:44 +02:00
Celine Mercier
b717e8bb8b Added properties for the OBIView class and cleaned up deprecated code 2016-09-28 14:26:23 +02:00
Celine Mercier
03a2c8ef7c Finished restructuring the OBIDMS_column class properties 2016-09-27 14:16:30 +02:00
Celine Mercier
a7f891d1c9 Added a lines_used property to the OBIDS_column class 2016-09-26 18:04:28 +02:00
Celine Mercier
bd50b3f972 Added version property to OBIDMS_column class 2016-09-26 17:45:10 +02:00
Celine Mercier
81380363b7 Added original_name property to OBIDMS_column class 2016-09-26 17:31:32 +02:00
Celine Mercier
a4b8349274 Added data_type property to OBIDMS_column class 2016-09-26 17:12:20 +02:00
Celine Mercier
a474391b27 Added nb_elements_per_line property to OBIDMS_column class 2016-09-26 17:01:13 +02:00
Celine Mercier
a0bc45cc92 Added elements_names property to OBIDMS_column class 2016-09-26 16:53:16 +02:00
Celine Mercier
76f89717fe Added alias property to OBIDMS_column cython class 2016-09-26 16:12:48 +02:00
Celine Mercier
b408a4f6eb Changed file name limits to adapt to system limits + minor changes 2016-09-22 18:05:07 +02:00
Celine Mercier
b083745f56 Deleted the "new line selection while editing a view" system 2016-09-22 11:19:29 +02:00
Celine Mercier
dd55aef3e5 Added column class method to get the unique references (name and 
version) of a column
 2016-09-21 17:08:44 +02:00
Celine Mercier
9ac522fde1 Better obi test command 2016-09-21 17:06:35 +02:00
Eric Coissac
6adb9eb623 Should solde issue #56 2016-09-19 21:40:40 +02:00
Celine Mercier
8f49553d5a First version of the obi test command, testing that the OBITools3 work 
correctly
 2016-09-15 12:26:07 +02:00
Celine Mercier
eb82d088cb Added some view class methods 2016-09-05 12:20:00 +02:00
Celine Mercier
8d360b0fac Minor improvements to obi export command 2016-08-19 17:49:22 +02:00
Celine Mercier
b34769b27c Minor improvements to obi export command 2016-08-19 17:46:55 +02:00