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 |
|
|
|
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 |
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
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 |
|
