obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity
953 Commits 18 Branches 66 Tags
3b3cf9359db382580d91cc64f9b365b5e84801dd
Commit Graph
100 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Celine Mercier 3b3cf9359d CMake: unset gcc for nix 2019-09-26 21:04:42 +02:00
Celine Mercier be85c55c9e Python: URIs: fixed bug on linux systems 2019-09-25 14:41:52 +02:00
Celine Mercier 6d5b904888 Cleaning 2019-09-25 11:58:00 +02:00
Celine Mercier 50e8374f6f Added website URL in readme file 2019-09-25 11:40:00 +02:00
Celine Mercier 6282242a04 C: Views: fixed a bug when trying to add a comment after changing the 
file name of a finished view
 2019-09-25 11:39:32 +02:00
Celine Mercier 44517db51f Fixed gcc warnings 2019-09-25 11:38:00 +02:00
Celine Mercier c3b9e46291 more cleaning 2019-09-24 13:58:53 +02:00
Celine Mercier 28b7fce59a Cython API: simpler column repr display 2019-09-22 20:23:31 +02:00
Celine Mercier fa9555deb9 obi stats: fixed bug with None values 2019-09-22 20:21:53 +02:00
Celine Mercier d30f7e7317 more cleaning 2019-09-22 18:52:05 +02:00
Celine Mercier 4fa38d9886 cleaning 2019-09-22 17:38:28 +02:00
Celine Mercier 71276537a6 obi import: fixed bug when importing a taxdump 2019-09-22 16:45:30 +02:00
Celine Mercier ba9ba7aa60 obi grep: now able to convert str to bytes in predicate expressions 2019-09-22 16:44:45 +02:00
Celine Mercier 7b4046c288 Bash completion script for commands, dms and views 2019-09-21 23:46:08 +02:00
Celine Mercier e2ba76002a Cleaned setup script and put to my name ;) 2019-09-21 23:44:24 +02:00
Celine Mercier 336100f716 obi less: now actually behaves like less 2019-09-21 18:29:12 +02:00
Celine Mercier d83398c0e0 Cython: View: lines from simple View instances are now displayed in tab 
instead of dict format
 2019-09-21 18:28:56 +02:00
Celine Mercier 974d25b815 Cython: Fixed bug in tab formatter with header option always being set 
to true
 2019-09-21 18:27:47 +02:00
Celine Mercier ec0737a600 Added signal catching and handling in C and Cython 2019-09-21 16:47:22 +02:00
Celine Mercier 06f9d6da60 obi import: importing a view to a DMS now uses the C API (more efficient 
and imports all metadata)
 2019-09-21 12:49:29 +02:00
Celine Mercier f0f7edf152 Python API: small option improvements 2019-09-21 12:08:36 +02:00
Celine Mercier 9e72c8d16a obi ls: improved taxonomy list 2019-09-20 20:46:33 +02:00
Celine Mercier 7c3fa14789 obi import: fixed bug when reading output URI 2019-09-20 20:43:48 +02:00
Celine Mercier ec874c095b new command: clean_dms to clean and unlock a DMS after a bad exit. 2019-09-20 20:38:25 +02:00
Celine Mercier 783a1343c4 DMS are now locked when used by a command. Added checks and changed 
cleaning mechanisms.
 2019-09-20 20:37:19 +02:00
Celine Mercier eb6c59dc1e obi import: proper check for taxonomy name already existing in DMS when 
importing a taxdump
 2019-09-17 13:41:49 +02:00
Celine Mercier ad46056179 obi export: if export format is not specified, it is guessed from the 
view type
 2019-09-17 13:22:41 +02:00
Celine Mercier 9063e9159d Export options: output option is now only non-positional for obi export 2019-09-17 13:19:17 +02:00
Celine Mercier 0159385943 URI decoding: fixed bug with dms-only URI 2019-09-17 12:50:37 +02:00
Celine Mercier a0c8deb806 obi export: made output to stdout and pipe in less possible 2019-09-17 12:31:03 +02:00
Celine Mercier f566618be6 Added option for no progress bar and made output URI option non 
positional (for stdout output)
 2019-09-17 12:29:33 +02:00
Celine Mercier 88451116e8 URIs: added stdout output (empty URI) 2019-09-17 12:28:10 +02:00
Celine Mercier eb913b2742 ecotag: trying to use a threshold lower than the ref db threshold now 
returns an error instead of a warning
 2019-09-15 19:27:47 +02:00
Celine Mercier f8d1fa678a obi stats: improved display with str instead of bytes 2019-09-10 16:20:36 +02:00
Celine Mercier bc55c5ef8c obi clean: fixed an openmp bug where the share size would be 0 blocking 
the program
 2019-09-10 15:37:33 +02:00
Celine Mercier f3b0e10c7f fixed a comment 2019-09-10 14:42:12 +02:00
Celine Mercier 8f9f2a2d10 obi ls: various improvements 2019-09-10 14:41:43 +02:00
Celine Mercier 045a751b0f Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2019-09-05 17:20:13 +02:00
Celine Mercier ad3a72597f Little fixes for linux compilation 2019-09-05 17:19:29 +02:00
Celine Mercier 8899478237 Update README.md 2019-09-04 17:29:45 +02:00
Celine Mercier ec614e5d15 Update README.md 2019-09-04 17:23:30 +02:00
Celine Mercier f8cccebe19 Update README.md 2019-09-04 17:11:46 +02:00
Celine Mercier 5e3c41b058 C: Fixed opened DIR leak 2019-09-04 16:48:13 +02:00
Celine Mercier b3a1011d36 C: fixed a bug when opening or creating a new column directory where the 
DMS was not saved in the struct
 2019-09-04 13:16:28 +02:00
Celine Mercier a7fabff1c7 C: made it so column DIR* are not kept open to handle very large DMS 2019-09-04 12:55:21 +02:00
Celine Mercier f296517716 Various display improvements 2019-09-03 21:46:39 +02:00
Celine Mercier d491480af2 C: fixed remaining memory bug in array indexer 2019-09-01 17:24:57 +02:00
Celine Mercier 073d98db08 C: ecotag: now prints a warning if the demanded threshold is lower than 
the db threshold
 2019-08-31 18:30:06 +02:00
Celine Mercier 0ee728c4d0 C: build_ref_db: now adds a comment with the threshold used to build the 
DB
 2019-08-31 18:29:40 +02:00
Celine Mercier 7423bacac0 C: Json comments: added an obi_read_comment function to read one value 
from comments
 2019-08-31 18:28:51 +02:00
Celine Mercier 53dcbc8ea3 Fixed log to be in str instead of bytes 2019-08-29 18:26:51 +02:00
Celine Mercier 4e75514bad obi import: fixed entry count 2019-08-29 18:26:09 +02:00
Celine Mercier 1ed2d45ac4 obi grep: made an error message clearer (error could be eventually be 
handled by program, looking for str in bytes returned by a column)
 2019-08-29 17:17:52 +02:00
Celine Mercier e43e49d6f1 C: optimized dir opening 2019-08-29 16:35:10 +02:00
Celine Mercier 187053026f Better detection of missing taxonomy 2019-08-29 16:10:09 +02:00
Celine Mercier dcf8cf1d64 Improved obi stats 2019-08-29 15:18:26 +02:00
Celine Mercier 3cfe3a9b00 Improved progress display when importing files in a DMS 2019-08-29 10:12:06 +02:00
Celine Mercier 728af51cb2 Python: better display of tuple values in fasta format 2019-08-28 15:55:36 +02:00
Celine Mercier 99a397b842 obi uniq: various improvements and fixes #66 2019-08-27 20:27:36 +02:00
Celine Mercier f5c472ffd1 C: fixed a memory bug in the array indexer 2019-08-27 20:26:46 +02:00
Celine Mercier 580db2f710 minor comment 2019-08-27 20:25:54 +02:00
Celine Mercier dbe09f83a2 Increased the threshold of elements per line in a column before they are 
stored as a character string
 2019-08-27 20:25:14 +02:00
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