|
|
2a4f1b8feb
|
obi import: now properly uses macros for column names
|
2019-03-15 11:39:21 +01:00 |
|
|
|
24a63f8732
|
URIs: URIs built with autocomplete now work too
|
2019-03-15 10:52:27 +01:00 |
|
|
|
478d19ab43
|
Cleaner stderr prints
|
2019-03-13 18:36:31 +01:00 |
|
|
|
e3c565d6be
|
Cleaner progress bar
|
2019-03-13 18:36:05 +01:00 |
|
|
|
d88390c6d8
|
Cython API: when importing a file in a DMS, its length is computed
beforehand for the progress bar
|
2019-03-13 18:35:32 +01:00 |
|
|
|
50e7cd61a6
|
added math.h import where needed
|
2019-03-13 11:17:25 +01:00 |
|
|
|
49d5f6fb1e
|
removed deprecated comment
|
2019-03-13 11:17:04 +01:00 |
|
|
|
b45c2ee653
|
Cython API: cleaner column rewriting API
|
2019-03-13 11:13:55 +01:00 |
|
|
|
6afd1294a7
|
Cython API: Views: fixed a bug when rewriting a column with different
attributes (last line is not written anymore)
|
2019-03-12 16:40:30 +01:00 |
|
|
|
a9ba7744cf
|
obidistutils: added fPIC flag needed for linux compilation and set
minimum python version to 3.7
|
2019-03-12 14:20:59 +01:00 |
|
|
|
185a95e667
|
cleaner Makefile
|
2019-03-11 15:20:10 +01:00 |
|
|
|
8835a1a983
|
removed -R compilaiton flag that gcc doesn't like
|
2019-03-07 15:55:46 +01:00 |
|
|
|
1ee50b7222
|
Fixed a bug when creating a column and checking the comments string if
it was NULL
|
2019-03-07 15:09:59 +01:00 |
|
|
|
720bb65b24
|
Installation: basic Makefile that creates the shared obi3 library used
by Cython
|
2019-03-07 14:01:37 +01:00 |
|
|
|
2a1ab9db29
|
Cython API, Views: guessing an obitype from a python value is now done
through the corresponding functions in utils
|
2019-03-07 13:57:37 +01:00 |
|
|
|
4bc52c08c2
|
minor changes
|
2019-03-07 13:53:37 +01:00 |
|
|
|
306da846e3
|
obidistutils: link obi3 C shared library instead of compiling all C
files with all modules (creating issues with global/static variables).
EXCEPT RUNTIME LINKING DOESN'T WORK YET
|
2019-03-07 13:50:29 +01:00 |
|
|
|
af57e532da
|
obidistutils: create doc/sphinx dir if needed
|
2019-03-07 13:47:23 +01:00 |
|
|
|
52de6f2717
|
Update distutils for openmp and new version of pip
|
2019-02-19 17:30:53 +01:00 |
|
|
|
29c56572cf
|
Add cfiles everywhere ;-)
|
2019-02-19 15:04:30 +01:00 |
|
|
|
de3d12af17
|
Renamed CAPI file
|
2019-02-19 14:50:30 +01:00 |
|
|
|
9ccddd5280
|
better cfiles
|
2019-02-19 14:11:29 +01:00 |
|
|
|
e026e9ec83
|
Fixed the new alignpaired end to work after ngsfilter with the 9879847
possible cases
|
2019-02-17 18:32:35 +01:00 |
|
|
|
4ddd1a1c37
|
embl iterator: only option on embl directories now works as intended
|
2019-02-12 16:46:08 +01:00 |
|
|
|
3015310535
|
Fixed a bug in kmer similarity computation where the fact that sequences
could be switched was not accounted for
|
2019-02-10 21:02:24 +01:00 |
|
|
|
08bcbcd357
|
ngsfilter: reworked to use apat library
|
2019-02-06 18:13:54 +01:00 |
|
|
|
04a3682307
|
Cython API: added API to use apat (pattern search) C library
|
2019-02-06 18:12:49 +01:00 |
|
|
|
6ca6d27ecb
|
ecoPCR: fixed amplicon length computation bug
|
2019-02-06 18:11:20 +01:00 |
|
|
|
8f18907566
|
Cython API: changed revcomp attribute of Nuc_Seq class to is_revcomp to
be more explicit
|
2019-02-06 18:09:11 +01:00 |
|
|
|
0b62619e4e
|
Various commentaries and insignificant fixes
|
2019-01-21 17:32:44 +01:00 |
|
|
|
c7f5b8d980
|
Alignpairedend: added alignment using shifting with best kmer similarity
(low level layer in C and Cython API)
|
2019-01-21 17:30:46 +01:00 |
|
|
|
59017c0d6b
|
C: taxonomy: fixed a bug when checking for root node
|
2019-01-21 17:23:25 +01:00 |
|
|
|
9f6bba183f
|
C: Added a function to get a nucleotide at a specific index in an
encoded sequence
|
2019-01-21 17:18:02 +01:00 |
|
|
|
2a6a112d29
|
obi import: fixed writing quality in views when appropriate (but still
not a satisfying solution)
|
2018-12-11 19:33:55 +01:00 |
|
|
|
c437931a35
|
Cython: fixed history dot graph for all views, and fixed history
recording for build_ref_db and ecotag
|
2018-12-10 17:09:00 +01:00 |
|
|
|
eb586b2f53
|
New command and C functions: obi ecotag
|
2018-12-09 19:19:32 +01:00 |
|
|
|
9556130b11
|
C obi_lcs: updated deprecated column names and associated comments
|
2018-12-09 19:17:13 +01:00 |
|
|
|
005aaeec06
|
C obi_lcs: fixed checking for identical sequences when aligning 2
columns
|
2018-12-09 19:16:44 +01:00 |
|
|
|
579f56bb54
|
obi align (pouic): fixed bug with the saved config when aligning 2
different views
|
2018-12-09 19:15:58 +01:00 |
|
|
|
da445066f3
|
C alignment filter: added a check for sequences not being equal when the
threshold requires that they are
|
2018-12-09 19:14:51 +01:00 |
|
|
|
0a407436da
|
C Views: made an error message more specific
|
2018-12-09 19:14:05 +01:00 |
|
|
|
54efff36c4
|
C build ref db: fixed 2 bugs when setting arrays: size of an element in
in bits not bytes and using view API instead of column API
|
2018-12-09 19:13:06 +01:00 |
|
|
|
6acb21712a
|
Missing commit for build_ref_db: C API file for cython
|
2018-12-09 19:11:59 +01:00 |
|
|
|
12087a6c3a
|
C, views: made 'view_exists' function public (now 'obi_view_exists')
|
2018-11-27 16:20:30 +01:00 |
|
|
|
fbabbceb5a
|
Fixed a bug in the array indexer where the value's length was no
properly set to 0 if the value was NA (ignore previous commit with the
same message)
|
2018-11-27 16:18:34 +01:00 |
|
|
|
6f27734d71
|
Cython: fxed a bug in INT tuple columns where values were converted to
double instead of int
|
2018-11-27 16:14:56 +01:00 |
|
|
|
b3bfa9ca65
|
Fixed a bug in the array indexer where the value's length was not
properly set to 0 if the value was NA
|
2018-11-27 16:12:41 +01:00 |
|
|
|
ece942e771
|
new command: build_ref_db to build a reference database with metadata
for the taxonomic assignment of sequences
|
2018-11-27 16:11:18 +01:00 |
|
|
|
ef8dc85f3c
|
C, taxonomy: new function to get the lowest common ancestor of two taxa
|
2018-11-27 16:00:29 +01:00 |
|
|
|
f942dd856f
|
C: new function to build a reference database with LCA and score
metadata for the taxonomic assignment of sequences
|
2018-11-27 15:56:50 +01:00 |
|
