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Author SHA1 Message Date
coissac daacd0df76 Strong refactoring 1 2016-12-26 13:35:31 +01:00
Celine Mercier 8e92bf6dac LCS alignment: it is now checked that sequences are not longer than what 
a 16 bits integer can code for (as the LCS and alignment lengths are
kept in 16 bits registers)
 2016-12-22 17:06:23 +01:00
Celine Mercier 30e4359c85 LCS alignment: documentation for all the lowest level functions 2016-12-22 17:03:51 +01:00
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
coissac 3cedd00d7f Add register function for column type 2016-12-20 11:13:57 +01:00
coissac 82fbe43980 transfert method to obiviews 2016-12-20 08:18:47 +01:00
coissac d1a972dfcb patch import 2016-12-20 08:15:42 +01:00
coissac f43dc3e3ab separate the obicolumn classes in new files 2016-12-20 08:15:08 +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 d99447c12b C function for LCS alignment of two columns, and optimized and fixed 
line count bug in function to align one column
 2016-12-16 19:39:02 +01:00
Celine Mercier 303bd6f445 Added function to build kmer table for 2 columns, and fixed bug (with 
line count) when building kmer table of one column
 2016-12-16 19:10:18 +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
coissac 04d39c62ab Try for a new API 2016-12-14 08:44:44 +01:00
Celine Mercier 9b24818fe2 Refactored alignment code for minimum redundancy between the function 
that aligns 1 column and the function that aligns 2 columns
 2016-12-13 17:18:12 +01:00
coissac 06cb7a9a58 Some change in the way to manage access to special items of the 
dictionary like sequence or quality
 2016-12-13 12:49:34 +01:00
coissac fc55fc117d Some cosmetic on the code 2016-12-13 12:48:13 +01:00
coissac 4ef5cb0d87 Move the OBIView_NUC_SEQS class to files _obiview_nuc_seq.pxd and 
_obiview_nuc_seq.pyx to avoid circular inclusion
 2016-12-13 12:46:49 +01:00
coissac fc805e5443 Remove some warnings in the editor 2016-12-13 08:29:22 +01:00
coissac 8d7ef7d3d1 patch the distutils to add the C source directory in the include path. 
This should solve most of the compilation problems related to .h files
located in this directory
 2016-12-13 08:02:09 +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 5e0c9f878b Added the doc for the function building the element names, and a missing 
free
 2016-12-05 10:46:21 +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 e60497651c Updated the documentation for the functions to set and get in the 
context of a view
 2016-11-30 12:22:47 +01:00
Celine Mercier 4ad8c16a73 Finished adding all the functions to directly set and get indices in 
columns containing indices referring to any type of data.
 2016-11-30 11:08:11 +01:00
Celine Mercier 6f6099687d Sequence alignment: if no sequence column is given and the view has the 
type NUC_SEQS_VIEW, the default sequence column is aligned
 2016-11-29 16:52:41 +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 5fb025f310 When aligning, it is now quickly checked whether the sequences are 
identical using their indexes
 2016-11-28 11:39:29 +01:00
Celine Mercier 8ce6f6c80b Added an argument to specify whether the two sequences can be identical 
when applying filters before aligning
 2016-11-28 11:38:02 +01:00
Celine Mercier 3e53f9418b Added functions to recover the indexes themselves from any column 
referring to indexed values
 2016-11-28 11:35:19 +01:00
Celine Mercier d40d2d0c76 Fixed error in documentation 2016-11-28 10:55:23 +01:00
Celine Mercier f897e87600 When closing a view, it is now automatically checked that all OBI_QUAL 
columns correspond to their associated OBI_SEQ column
 2016-11-25 12:04:57 +01:00
Celine Mercier 70e056a2aa It is now impossible to open or clone a view that is not finished (= has 
been closed at least once)
 2016-11-24 11:19:07 +01:00
Celine Mercier 8abbfa203a Good file for commit 6fa9a8bd: When a view is cloned, a comment is added 
to the new view specifying the name of the cloned view
 2016-11-23 11:32:39 +01:00
Celine Mercier 6fa9a8bd76 When a view is cloned, a comment is added to the new view specifying the 
name of the cloned view
 2016-11-23 11:29:21 +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 0ab9e6c05a When adding an existing column to a view, it is checked that the 
column's line count is at least the view's line count. This can't be
more stringent for reasons that need to be rediscussed
 2016-11-23 11:04:53 +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 08e67a090f Changed the inline functions syntax, which should make it compatible 
with more compilers
 2016-11-18 16:21:26 +01:00
Celine Mercier 621b4972db Functions to get obiblobs through views 2016-11-18 15:59:50 +01:00
Celine Mercier 7d022c1a52 If the indexer name is NULL when creating a column, it now becomes the 
column name
 2016-11-18 15:56:51 +01:00
Celine Mercier 1c71c195fc Goes with a0ebc2d8 2016-11-10 15:01:29 +01:00
Celine Mercier 54cfeffd85 Goes with 8f724f4f, forgotten file 2016-11-10 14:48:31 +01:00
Celine Mercier a0ebc2d871 Functions to directly retrieve Obiblobs from indexers 2016-11-10 14:45:28 +01:00
Celine Mercier 8f724f4f8e Some code refactoring 2016-11-09 16:48:00 +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