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Author SHA1 Message Date
Celine Mercier 3d1b2e8ed9 Better handling of column lines with all values at NA 2019-08-27 20:20:26 +02:00
Celine Mercier ae5f42c260 fixes #61 : now reading merged taxids information when building a 
reference database
 2019-08-19 12:30:56 +02:00
Celine Mercier af7cecf59f Fixed a bug where a directory was not closed properly resulting in errno 
24 sometimes
 2019-08-18 19:46:52 +02:00
Celine Mercier 5f20be44b2 Minor fixes 2019-08-18 19:45:53 +02:00
Celine Mercier 66441e0aef Fixed a bug when sending a DMS path to a C function from Cython 2019-08-18 19:43:51 +02:00
Celine Mercier 13952358b3 Fixed a bug where some commands wouldn't work if the input DMS was not 
in the current directory
 2019-07-25 11:59:19 +02:00
Celine Mercier 9f38cd8cf6 updated a comment 2019-07-23 19:03:24 +02:00
Celine Mercier 946f9723b8 ecotag: fixed a bug where the wrong taxid for the best match was 
retrieved
 2019-07-23 19:02:17 +02:00
Celine Mercier 9752ff8494 embl parser: information display about progress when parsing multiple 
files
 2019-07-23 18:59:07 +02:00
Celine Mercier d99702f56f ngsfilter and alignpairedend: paired-end reads are now correctly 
reversed and labeled to be aligned correctly by alignpairedend
 2019-07-23 18:56:51 +02:00
Celine Mercier 1759302829 C: ecotag: fixed 2 memory bugs 2019-07-06 16:31:19 +02:00
Celine Mercier 86bfa96fbe C: kmer similarity: small improvements 2019-07-06 16:30:32 +02:00
Celine Mercier f765c6f41e obi alignpairedend: fixed a bug where first seq was kept in result view 
instead of consensus seq
 2019-07-06 16:29:32 +02:00
Celine Mercier a83bf43ab9 obi stats: result display is now sorted 2019-07-06 16:27:51 +02:00
Celine Mercier 3d9f0352ff obiclean parallelized 2019-06-20 19:44:04 +02:00
Celine Mercier 9b4c3537f9 multithreaded obiclean working but not cleaned 2019-06-19 17:29:58 +02:00
Celine Mercier fd0b7a9177 j loop with critical (untested) 2019-06-04 17:14:36 +02:00
Celine Mercier debf59b266 i loop parallelized: bad 2019-05-25 18:37:56 +02:00
Celine Mercier a04588da31 openmp on j loop (i loop probably better) 2019-05-24 16:51:04 +02:00
Celine Mercier ed5bb70c80 CMake: setting compiler higher to avoid conflicts, and linking libopenmp 2019-05-22 16:26:30 +02:00
Celine Mercier 22a5ae72d1 obi clean: not using tsearch library anymore, a simple byte array 
instead. A lot more time and memory efficient. Closes #67
 2019-05-19 17:39:53 +02:00
Celine Mercier 3afbbeb7e5 CMake: made required version 3.10 for ubuntu 2019-03-31 16:54:05 +02:00
Celine Mercier d6056a8e50 dirty temporary fix for install 2019-03-31 16:19:05 +02:00
Celine Mercier ac47bdce5d history: fixed DMS history when multiple inputs 2019-03-31 15:44:20 +02:00
Celine Mercier 7f8d1e7196 C: obi lcs: cleaner progress print 2019-03-31 15:42:58 +02:00
Celine Mercier 80068a3c19 ngsfilter: fixed parsing error 2019-03-31 15:42:30 +02:00
Celine Mercier a3e6b7d913 obi import: fixed import of View_NUC_SEQS to another DMS 2019-03-31 15:42:07 +02:00
Celine Mercier 416c2d7ba0 Cython: made fasta formatter cleaner 2019-03-31 15:41:32 +02:00
Celine Mercier 26fb149efb C: made build_ref_db cleaner 2019-03-31 15:40:13 +02:00
Celine Mercier 2b8c066f8e Cython: added possibility to output in tabular format 2019-03-31 15:39:38 +02:00
Celine Mercier e39c1a7fbf Cython: added tab formatter and parser (for obi export) 2019-03-31 15:38:34 +02:00
Celine Mercier 6841d879aa obi history: fixed a bug when displaying ascii history 2019-03-31 10:51:52 +02:00
Celine Mercier f0ff585455 Removing trace 2019-03-30 20:52:54 +01:00
Celine Mercier 601a2cfd7d obi uniq: various fixes... 2019-03-30 20:34:53 +01:00
Celine Mercier 7c518300a0 C: Views: fixed a bug when creating automatic columns with unformatted 
comments
 2019-03-30 20:33:14 +01:00
Celine Mercier f16bbca8e2 obi grep: fixed a bug where -p option didn't work 2019-03-30 19:10:42 +01:00
Celine Mercier 173483448a Merge commit '3d842ff7' 2019-03-30 15:29:52 +01:00
Celine Mercier 52b3a9fc39 C: taxonomy: fixed a segfault on linux when trying to fclose an unopened 
file
 2019-03-30 15:19:12 +01:00
Celine Mercier ce686e9569 obi import: progress bar fixed when using --only option 2019-03-30 15:16:57 +01:00
Celine Mercier c293cfabbb Python: embl parser: fixed a bug preventing taxids from being parsed 2019-03-30 15:15:49 +01:00
Celine Mercier 0847d618d6 fixed typo 2019-03-30 15:14:30 +01:00
Celine Mercier 9fcebd7643 C: build_reference_db: made some errors more explicit 2019-03-30 15:11:49 +01:00
Celine Mercier ee9947217c alignpairedend: fixed the worst memory leak and the handling of the case 
where 0 common kmers are found
 2019-03-29 11:16:25 +01:00
Celine Mercier ceaafca427 ngsfilter: fixed a bug (maybe 2) in the algo for the choice of the 
reverse primer when running on unaligned sequences
 2019-03-29 10:56:17 +01:00
Celine Mercier 7c2787b6b3 trying to fix cython difficulties 2019-03-26 16:19:55 +01:00
Celine Mercier 5a05258fcb fixed relative cython imports to be absolute 2019-03-26 15:52:59 +01:00
Celine Mercier 8e70bf1ee1 obi import: fixed bug when rewriting a column (keeping wrong type in 
import module)
 2019-03-26 14:56:18 +01:00
Celine Mercier d8a7bd42bd Cython API, taxonomy: fixed parental tree iterator (skipped second to 
last taxon, in OBI1 too)
 2019-03-26 14:08:54 +01:00
Celine Mercier 06178d9d61 Genbank file parser functions that should have been included in a 
previous commit
 2019-03-20 11:44:43 +01:00
Celine Mercier 3abe1b7ace obi_errno_to_exception function now properly reads obi_errno global 
variable directly
 2019-03-20 11:43:12 +01:00
Celine Mercier 802a3f5933 data import: entries now counted if there are multiple files 2019-03-18 18:16:39 +01:00
Celine Mercier 7e20870719 Added genbank parser 2019-03-15 16:06:27 +01:00
Celine Mercier e8090a44c9 Fixed the ultimate bug with embl (and genbank) parsers: raising any 
exception in a python generator makes it unable to resume. So now,
exceptions are not raised but printed, then functions return None and
that's handled at higher level.
 2019-03-15 16:06:06 +01:00
Celine Mercier 832f582802 Fixed no-skip-on-error option :p 2019-03-15 16:04:04 +01:00
Celine Mercier 58d0c850c2 Made skip on error option True by default...... 2019-03-15 15:50:40 +01:00
Celine Mercier 7737211ac2 Small fix in embl and genbank features parser 2019-03-15 15:50:11 +01:00
Celine Mercier c953f0cb00 Fixed embl import where sequences were not imported as Nuc_Seq objects 2019-03-15 11:41:07 +01:00
Celine Mercier bb045c3ae9 added TAXID_COLUMN to C API declarations for Cython 2019-03-15 11:40:06 +01:00
Celine Mercier 2a4f1b8feb obi import: now properly uses macros for column names 2019-03-15 11:39:21 +01:00
Celine Mercier 24a63f8732 URIs: URIs built with autocomplete now work too 2019-03-15 10:52:27 +01:00
Celine Mercier 478d19ab43 Cleaner stderr prints 2019-03-13 18:36:31 +01:00
Celine Mercier e3c565d6be Cleaner progress bar 2019-03-13 18:36:05 +01:00
Celine Mercier 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
Celine Mercier 50e7cd61a6 added math.h import where needed 2019-03-13 11:17:25 +01:00
Celine Mercier 49d5f6fb1e removed deprecated comment 2019-03-13 11:17:04 +01:00
Celine Mercier b45c2ee653 Cython API: cleaner column rewriting API 2019-03-13 11:13:55 +01:00
Celine Mercier 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
Celine Mercier 185a95e667 cleaner Makefile 2019-03-11 15:20:10 +01:00
Celine Mercier 8835a1a983 removed -R compilaiton flag that gcc doesn't like 2019-03-07 15:55:46 +01:00
Celine Mercier 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
Celine Mercier 720bb65b24 Installation: basic Makefile that creates the shared obi3 library used 
by Cython
 2019-03-07 14:01:37 +01:00
Celine Mercier 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
Celine Mercier 4bc52c08c2 minor changes 2019-03-07 13:53:37 +01:00
Celine Mercier 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
Celine Mercier af57e532da obidistutils: create doc/sphinx dir if needed 2019-03-07 13:47:23 +01:00
Celine Mercier de3d12af17 Renamed CAPI file 2019-02-19 14:50:30 +01:00
Celine Mercier 9ccddd5280 better cfiles 2019-02-19 14:11:29 +01:00
Celine Mercier e026e9ec83 Fixed the new alignpaired end to work after ngsfilter with the 9879847 
possible cases
 2019-02-17 18:32:35 +01:00
Celine Mercier 4ddd1a1c37 embl iterator: only option on embl directories now works as intended 2019-02-12 16:46:08 +01:00
Celine Mercier 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
Celine Mercier 08bcbcd357 ngsfilter: reworked to use apat library 2019-02-06 18:13:54 +01:00
Celine Mercier 04a3682307 Cython API: added API to use apat (pattern search) C library 2019-02-06 18:12:49 +01:00
Celine Mercier 6ca6d27ecb ecoPCR: fixed amplicon length computation bug 2019-02-06 18:11:20 +01:00
Celine Mercier 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
Celine Mercier 0b62619e4e Various commentaries and insignificant fixes 2019-01-21 17:32:44 +01:00
Celine Mercier 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
Celine Mercier 59017c0d6b C: taxonomy: fixed a bug when checking for root node 2019-01-21 17:23:25 +01:00
Celine Mercier 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
Celine Mercier 2a6a112d29 obi import: fixed writing quality in views when appropriate (but still 
not a satisfying solution)
 2018-12-11 19:33:55 +01:00
Celine Mercier 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
Celine Mercier eb586b2f53 New command and C functions: obi ecotag 2018-12-09 19:19:32 +01:00
Celine Mercier 9556130b11 C obi_lcs: updated deprecated column names and associated comments 2018-12-09 19:17:13 +01:00
Celine Mercier 005aaeec06 C obi_lcs: fixed checking for identical sequences when aligning 2 
columns
 2018-12-09 19:16:44 +01:00
Celine Mercier 579f56bb54 obi align (pouic): fixed bug with the saved config when aligning 2 
different views
 2018-12-09 19:15:58 +01:00
Celine Mercier 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
Celine Mercier 0a407436da C Views: made an error message more specific 2018-12-09 19:14:05 +01:00
Celine Mercier 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
Celine Mercier 6acb21712a Missing commit for build_ref_db: C API file for cython 2018-12-09 19:11:59 +01:00
Celine Mercier 12087a6c3a C, views: made 'view_exists' function public (now 'obi_view_exists') 2018-11-27 16:20:30 +01:00
Celine Mercier 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