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Author SHA1 Message Date
Celine Mercier f0d152fcbd ngsfilter: now checking primer length (fixes #75) 2020-04-05 18:29:10 +02:00
Celine Mercier 8019dee68e ecotag: now closing all DMS properly 2020-04-05 13:20:49 +02:00
Celine Mercier 0b4a234671 Swich to version 3.0.0-beta11 2020-02-12 14:23:42 +01:00
Celine Mercier d32cfdcce5 ecotag: fixed the generated column comments formatting that would 
generate errors
 2020-02-12 14:23:17 +01:00
Celine Mercier 219c0d6fdc obi cat: Fixed the handling when concatenating views with dictionaries 
having different key sets
 2020-02-12 14:21:39 +01:00
Celine Mercier dc9f897917 switch to version 3.0.0-beta10 2020-02-02 21:15:27 +01:00
Celine Mercier bb72682f7d obi import: new option --preread to do a first readthrough of the 
dataset if it contains huge dictionaries for a much faster import.
 2020-02-02 21:12:34 +01:00
Celine Mercier 52920c3c71 URI decoding: dirty temp fix for bug where default dms makes a mess when 
should guess file
 2020-02-02 21:11:05 +01:00
Celine Mercier 18c22cecf9 switch to version 3.0.0-beta9 2020-02-01 15:48:55 +01:00
Celine Mercier 1bfb96023c obi import: rewriting a column now deletes the old one to save disk 
space
 2020-02-01 15:31:14 +01:00
Celine Mercier c67d668989 obi import: fixed a bug when the first entry would contain a dictionary 
with one key. Switch to beta8
 2020-01-29 20:23:39 +01:00
Celine Mercier db0ac37d41 switch to version 3.0.0-beta7 2020-01-29 16:18:53 +01:00
Celine Mercier d0c21ecd39 Removed an OpenMP clause that was not obligatory and triggered a known 
gcc bug involving macros
 2020-01-24 16:00:53 +01:00
Celine Mercier 53212168a2 History: added 'obi' in bash history for practical reasons 2020-01-23 16:51:49 +01:00
Celine Mercier b4b2e62195 Cleaner handling of reverse quality columns 2020-01-18 19:28:12 +01:00
Celine Mercier ced82c4242 Switching to version 3.0-beta6 2020-01-18 17:29:23 +01:00
Celine Mercier a524f8829e New command: obi cat to concatenate views (not optimized yet) 2020-01-18 17:28:31 +01:00
Celine Mercier 5c9091e9eb C: closing DMS after cleaning it instead of counting on upper layer 2020-01-18 17:27:35 +01:00
Celine Mercier 822000cb70 Fixes in documentation 2020-01-18 17:26:18 +01:00
Celine Mercier b9cd9bee9a C: Changed obibool definitions because of conflict with R 2020-01-06 15:11:31 +01:00
Celine Mercier b1f3e082f9 ngsfilter: fixed a bug when there is only one tag introduced in latest 
edit
 2020-01-06 13:53:38 +01:00
Celine Mercier 6c018b403c ecopcr: fixed and improved the options to keep nuclotides around the 
amplicon
 2019-12-26 20:45:54 +01:00
Celine Mercier 694d1934a8 Tagging version beta3 2019-12-12 17:03:13 +01:00
Celine Mercier fc3ac03630 clean_dms: now works with extension 2019-12-12 17:02:50 +01:00
Celine Mercier d75e54a078 uniq: added forced deletion of reverse sequence quality 2019-12-12 17:02:36 +01:00
Celine Mercier 6bfd7441f3 ngsfilter: fixed sequence cutting when dealing with unaligned sequences. 
Could use optimization
 2019-12-12 17:01:31 +01:00
Celine Mercier 81a179239c ngsfilter: fixed sequence cut bug on aligned sequences. Still exists for 
unaligned sequences
 2019-12-10 18:13:27 +01:00
Celine Mercier 35ce37c0f7 ngsfilter: fixed a bug with unaligned chimeras (unpaired primers) and 
made error annotations more explicit
 2019-12-10 13:43:32 +01:00
Celine Mercier 53f18316b0 ngsfilter: made more robust and practical to use with empty tags 2019-11-29 15:21:08 +01:00
Celine Mercier 8bc249b2f4 Version 3.0.0-beta1 2019-09-27 14:52:05 +02:00
Celine Mercier e308c2e822 versioning 1.0.beta 2019-09-26 21:05:05 +02:00
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