|
|
f5e992abbf
|
Added a check on the element when setting a value in a column
|
2017-07-05 14:49:20 +02:00 |
|
|
|
1d2996c6c0
|
Better handling and tracing of Index Errors between C and Cython
|
2017-07-05 14:45:43 +02:00 |
|
|
|
71b1a43df8
|
Added functions to clone views with a simpler API
|
2017-04-21 11:58:15 +02:00 |
|
|
|
2f0c4b90d7
|
Fixed a problem where a view would have a wrong line count after adding
a first column to it if there was already a Line selection associated
(happening when cloning), and fixed a bad error check.
|
2017-04-14 16:25:55 +02:00 |
|
|
|
537b9847da
|
Minor C doc clarification
|
2017-04-14 16:23:17 +02:00 |
|
|
|
ad8de80353
|
Views: better checks when adding an existing column to a view
|
2017-04-06 14:44:07 +02:00 |
|
|
|
778acc48cd
|
Added linked lists to handle lists of column pointers in views (not
tested)
|
2017-03-06 16:06:17 +01:00 |
|
|
|
3319ede837
|
Views: Column dictionaries now store and return pointers on column
pointers instead of column pointers.
|
2017-02-22 13:49:50 +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 |
|
|
|
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 |
|
|
|
a9102620f5
|
Fixed missing email address
|
2017-02-07 17:14:10 +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 |
|
|
|
651c1d7845
|
utilities: bsearch and qsort with additional user_data pointer argument
|
2017-01-31 16:45:47 +01:00 |
|
|
|
c0bcdce724
|
Taxonomy: documentation for all the functions, and fixed bugs when
closing the taxonomy (overwriting of .pdx files, missing freeing, and
re-placed a misplaced condition)
|
2017-01-18 18:22:49 +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 |
|
|
|
0385a92e02
|
Taxonomy: Refactored the taxdump reading, and little fixes
|
2017-01-11 16:36:08 +01:00 |
|
|
|
41ad3deec0
|
Taxonomy: informations about deleted taxids is now read from
delnodes.dmp file and added to *.adx file
|
2017-01-09 17:28:49 +01:00 |
|
|
|
d68374018b
|
Taxonomy: functions to read the *.adx file (containing the deprecated
and current taxids and their corresponding indices in the taxa
structure) and to find the taxa using the merged index.
|
2017-01-06 15:52:21 +01:00 |
|
|
|
f396625f98
|
Taxonomy: function to write *.adx files
|
2017-01-05 15:37:13 +01:00 |
|
|
|
897032387f
|
Taxonomy: reading merged.dmp file in taxdump
|
2017-01-05 14:28:36 +01:00 |
|
|
|
daacd0df76
|
Strong refactoring 1
|
2016-12-26 13:35:31 +01:00 |
|
|
|
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 |
|
|
|
30e4359c85
|
LCS alignment: documentation for all the lowest level functions
|
2016-12-22 17:03:51 +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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
936be64c34
|
Goes with 5e0c9f87 (missing ';' and fixed compilation warnings)
|
2016-12-05 11:18:29 +01:00 |
|
|
|
5e0c9f878b
|
Added the doc for the function building the element names, and a missing
free
|
2016-12-05 10:46:21 +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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
5fb025f310
|
When aligning, it is now quickly checked whether the sequences are
identical using their indexes
|
2016-11-28 11:39:29 +01:00 |
|
|
|
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 |
|
|
|
3e53f9418b
|
Added functions to recover the indexes themselves from any column
referring to indexed values
|
2016-11-28 11:35:19 +01:00 |
|
|
|
d40d2d0c76
|
Fixed error in documentation
|
2016-11-28 10:55:23 +01:00 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
08e67a090f
|
Changed the inline functions syntax, which should make it compatible
with more compilers
|
2016-11-18 16:21:26 +01:00 |
|
|
|
621b4972db
|
Functions to get obiblobs through views
|
2016-11-18 15:59:50 +01:00 |
|
|
|
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 |
|
|
|
1c71c195fc
|
Goes with a0ebc2d8
|
2016-11-10 15:01:29 +01:00 |
|
|
|
54cfeffd85
|
Goes with 8f724f4f, forgotten file
|
2016-11-10 14:48:31 +01:00 |
|
