|
|
fc20b83ad1
|
Merging
|
2017-02-20 14:56:04 +01:00 |
|
|
|
431c1c8c6a
|
Merge branch 'Eric_new_Python_API' of
git@git.metabarcoding.org:obitools/obitools3.git into
Eric_new_Python_API
Conflicts:
python/obitools3/obidms/_obidms.pxd
python/obitools3/obidms/_obidms.pyx
python/obitools3/obidms/_obidmscolumn_bool.pyx
python/obitools3/obidms/_obidmscolumn_str.pyx
python/obitools3/obidms/_obiseq.pxd
python/obitools3/obidms/_obiseq.pyx
python/obitools3/obidms/_obitaxo.pxd
python/obitools3/obidms/_obitaxo.pyx
python/obitools3/obidms/_obiview.pxd
python/obitools3/obidms/_obiview.pyx
python/obitools3/obidms/_obiview_nuc_seq.pxd
python/obitools3/obidms/_obiview_nuc_seq.pyx
python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
python/obitools3/obidms/capi/obialign.pxd
python/obitools3/obidms/capi/obidmscolumn.pxd
python/obitools3/obidms/capi/obitaxonomy.pxd
python/obitools3/obidms/capi/obiview.pxd
|
2017-02-20 14:55:36 +01:00 |
|
|
|
f23315e26f
|
New Cython API: compile but doesn't work
|
2017-02-17 15:14:06 +01:00 |
|
|
|
071a3b61ab
|
Merged master fixed conflict.
|
2017-02-14 10:58:43 +01:00 |
|
|
|
e524041013
|
Views: Files for unfinished views now have the extension
'.obiview_unfinished', renamed to '.obiview' when the view is finished.
|
2017-02-07 17:16:09 +01:00 |
|
|
|
7e9932f488
|
Fixed a C function declaration
|
2017-02-07 17:12:56 +01:00 |
|
|
|
e50da64ea1
|
The elements names when a column contains several elements per line are
now formatted with '\0' as separator and handled in a more optimized way
|
2017-01-31 16:48:06 +01:00 |
|
|
|
c065c1914a
|
Taxonomy: adding, writing and reading preferred names, changed some
function names, and fixed a bug with taxa indices not being properly
initialized
|
2017-01-16 17:28:20 +01:00 |
|
|
|
cf7f2de016
|
Modify __init__ and close method to deal with registration process
|
2017-01-10 14:26:16 +01:00 |
|
|
|
4b02ba73ac
|
Add the OBIObject concept
|
2017-01-10 14:07:10 +01:00 |
|
|
|
4a1d3167a7
|
Last change on my branch
|
2017-01-02 16:46:52 +01:00 |
|
|
|
2139bfc748
|
refactoring...
|
2017-01-02 13:05:22 +01:00 |
|
|
|
65f3b16e6d
|
Refactoring ...
|
2016-12-29 18:22:05 +01:00 |
|
|
|
0526386337
|
first working DMS class
|
2016-12-27 06:17:45 +01:00 |
|
|
|
62caf1346e
|
temporary remove some files
|
2016-12-26 15:03:24 +01:00 |
|
|
|
3ac6e85fb3
|
Big refactoring 4
|
2016-12-26 14:58:03 +01:00 |
|
|
|
5156f6bb9e
|
Big refactoring 3
|
2016-12-26 14:18:01 +01:00 |
|
|
|
e6db2086d5
|
Big refactoring 2
|
2016-12-26 13:56:31 +01:00 |
|
|
|
daacd0df76
|
Strong refactoring 1
|
2016-12-26 13:35:31 +01:00 |
|
|
|
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 |
|
|
|
3cedd00d7f
|
Add register function for column type
|
2016-12-20 11:13:57 +01:00 |
|
|
|
82fbe43980
|
transfert method to obiviews
|
2016-12-20 08:18:47 +01:00 |
|
|
|
d1a972dfcb
|
patch import
|
2016-12-20 08:15:42 +01:00 |
|
|
|
f43dc3e3ab
|
separate the obicolumn classes in new files
|
2016-12-20 08:15:08 +01:00 |
|
|
|
9c71b06117
|
Removed deprecated TODOs
|
2016-12-19 14:36:40 +01:00 |
|
|
|
3bf5260174
|
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
|
2016-12-19 10:31:18 +01:00 |
|
|
|
857a5198e4
|
Updated `obi lcs` for the LCS alignment of two columns
|
2016-12-16 19:40:36 +01:00 |
|
|
|
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 |
|
|
|
191c83aafc
|
Added missing *.cfiles
|
2016-12-15 15:28:34 +01:00 |
|
|
|
04d39c62ab
|
Try for a new API
|
2016-12-14 08:44:44 +01:00 |
|
|
|
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 |
|
|
|
fc55fc117d
|
Some cosmetic on the code
|
2016-12-13 12:48:13 +01:00 |
|
|
|
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 |
|
|
|
fc805e5443
|
Remove some warnings in the editor
|
2016-12-13 08:29:22 +01:00 |
|
|
|
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 |
|
|
|
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 |
|
|
|
936be64c34
|
Goes with 5e0c9f87 (missing ';' and fixed compilation warnings)
|
2016-12-05 11:18:29 +01:00 |
|
|
|
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 |
|
|
|
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 |
|
|
|
76a4c6b14e
|
Fixed a bug when cloning a view and checking its type
|
2016-11-23 11:28:17 +01:00 |
|
|
|
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 |
|
|
|
1c71c195fc
|
Goes with a0ebc2d8
|
2016-11-10 15:01:29 +01:00 |
|
|
|
359578814b
|
Added view type property to OBIView cython class and updated obi export
to use it
|
2016-11-08 17:49:59 +01:00 |
|
|
|
51b23915ca
|
Added properties for Nuc_Seq cython classes (and updated commands using
them)
|
2016-11-08 16:59:32 +01:00 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
4bc19c3e49
|
obi export: view type is now checked and progress bar functioning
|
2016-11-08 11:17:20 +01:00 |
|
|
|
2d2fe5279d
|
Added functions to add new taxa to a taxonomy with handling of
associated *.ldx files
|
2016-11-03 17:59:21 +01:00 |
|
|
|
2504bf0fa9
|
Added an iterator to the OBI_Taxonomy cython class
|
2016-11-02 11:08:18 +01:00 |
|
