obitools/obitools3
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  • 343999a627 Taxonomy: fixed a critical memory bug when building the list of merged taxids Celine Mercier 2020-04-15 17:46:13 +02:00
  • e9a40630e9 C: Columns: rounding column growth to ceil to avoid looping on small values Celine Mercier 2020-04-13 19:02:10 +02:00
  • 8dbcd3025a C: Columns: reduced column growth factor from 2 to 1.3 to avoid errno28 Celine Mercier 2020-04-13 14:47:56 +02:00
  • 4cf635d001 Switch to version 3.0.0-beta13 v3.0.0-beta13 Celine Mercier 2020-04-12 17:42:58 +02:00
  • b7e7cc232a Made completion script cleaner Celine Mercier 2020-04-12 17:41:59 +02:00
  • b6ab792ceb C: made error message more detailed when checking that sequences and qualities match Celine Mercier 2020-04-12 17:40:24 +02:00
  • ddea5a2964 obi import: fixed inconsequential error when precomputing number of entries in some formats Celine Mercier 2020-04-12 17:38:42 +02:00
  • 30852ab7d5 View bash history: removed useless shebang Celine Mercier 2020-04-12 17:36:04 +02:00
  • 4d0299904e all commands (almost): cleaner DMS closing at the end Celine Mercier 2020-04-12 17:31:58 +02:00
  • eef5156d95 obi stats: fixed error when printing bool keys Celine Mercier 2020-04-12 17:12:04 +02:00
  • e62c991bbc goes with previous commit Celine Mercier 2020-04-10 11:22:26 +02:00
  • 1218eed7fd ecopcr: now printing a warning instead of interrupting with an error when a taxid is not found Celine Mercier 2020-04-10 11:22:04 +02:00
  • cd9cea8c97 obi import: fixed critical bug where the last entry of embl and genbank files was not imported Celine Mercier 2020-04-09 19:26:27 +02:00
  • 98cfb70d73 ecopcr: made some errors more informative Celine Mercier 2020-04-09 09:15:28 +02:00
  • b9f68c76c8 ecopcr: added warnings and check of primer length (related to #75) Celine Mercier 2020-04-05 18:40:56 +02:00
  • 0b98371688 ngsfilter: added warning about primer length in -h (#75) Celine Mercier 2020-04-05 18:39:20 +02:00
  • f0d152fcbd ngsfilter: now checking primer length (fixes #75) Celine Mercier 2020-04-05 18:29:10 +02:00
  • 8019dee68e ecotag: now closing all DMS properly Celine Mercier 2020-04-05 13:20:49 +02:00
  • 0b4a234671 Swich to version 3.0.0-beta11 v3.0.0-beta11 Celine Mercier 2020-02-12 14:23:42 +01:00
  • d32cfdcce5 ecotag: fixed the generated column comments formatting that would generate errors Celine Mercier 2020-02-12 14:23:17 +01:00
  • 219c0d6fdc obi cat: Fixed the handling when concatenating views with dictionaries having different key sets Celine Mercier 2020-02-12 14:21:39 +01:00
  • dc9f897917 switch to version 3.0.0-beta10 v3.0.0-beta10 Celine Mercier 2020-02-02 21:15:27 +01:00
  • bb72682f7d obi import: new option --preread to do a first readthrough of the dataset if it contains huge dictionaries for a much faster import. Celine Mercier 2020-02-02 21:12:34 +01:00
  • 52920c3c71 URI decoding: dirty temp fix for bug where default dms makes a mess when should guess file Celine Mercier 2020-02-02 21:11:05 +01:00
  • 18c22cecf9 switch to version 3.0.0-beta9 v3.0.0-beta9 Celine Mercier 2020-02-01 15:48:55 +01:00
  • 1bfb96023c obi import: rewriting a column now deletes the old one to save disk space Celine Mercier 2020-02-01 15:31:14 +01:00
  • c67d668989 obi import: fixed a bug when the first entry would contain a dictionary with one key. Switch to beta8 v3.0.0-beta8 Celine Mercier 2020-01-29 20:23:39 +01:00
  • db0ac37d41 switch to version 3.0.0-beta7 v3.0.0-beta7 Celine Mercier 2020-01-29 16:18:53 +01:00
  • d0c21ecd39 Removed an OpenMP clause that was not obligatory and triggered a known gcc bug involving macros Celine Mercier 2020-01-24 16:00:53 +01:00
  • 53212168a2 History: added 'obi' in bash history for practical reasons Celine Mercier 2020-01-23 16:51:49 +01:00
  • b4b2e62195 Cleaner handling of reverse quality columns v3.0.0-beta6 Celine Mercier 2020-01-18 19:28:12 +01:00
  • ced82c4242 Switching to version 3.0-beta6 Celine Mercier 2020-01-18 17:29:23 +01:00
  • a524f8829e New command: obi cat to concatenate views (not optimized yet) Celine Mercier 2020-01-18 17:28:31 +01:00
  • 5c9091e9eb C: closing DMS after cleaning it instead of counting on upper layer Celine Mercier 2020-01-18 17:27:35 +01:00
  • 822000cb70 Fixes in documentation Celine Mercier 2020-01-18 17:26:18 +01:00
  • b9cd9bee9a C: Changed obibool definitions because of conflict with R Celine Mercier 2020-01-06 15:11:31 +01:00
  • b1f3e082f9 ngsfilter: fixed a bug when there is only one tag introduced in latest edit v3.0.0-beta5 Celine Mercier 2020-01-06 13:53:38 +01:00
  • 6c018b403c ecopcr: fixed and improved the options to keep nuclotides around the amplicon v3.0.0-beta4 Celine Mercier 2019-12-26 20:45:54 +01:00
  • 694d1934a8 Tagging version beta3 3.0.0-beta3 Celine Mercier 2019-12-12 17:03:13 +01:00
  • fc3ac03630 clean_dms: now works with extension Celine Mercier 2019-12-12 17:02:50 +01:00
  • d75e54a078 uniq: added forced deletion of reverse sequence quality Celine Mercier 2019-12-12 17:02:36 +01:00
  • 6bfd7441f3 ngsfilter: fixed sequence cutting when dealing with unaligned sequences. Could use optimization Celine Mercier 2019-12-12 17:01:31 +01:00
  • 81a179239c ngsfilter: fixed sequence cut bug on aligned sequences. Still exists for unaligned sequences Celine Mercier 2019-12-10 18:13:27 +01:00
  • 35ce37c0f7 ngsfilter: fixed a bug with unaligned chimeras (unpaired primers) and made error annotations more explicit v3.0.0-beta2 Celine Mercier 2019-12-10 13:43:32 +01:00
  • 53f18316b0 ngsfilter: made more robust and practical to use with empty tags Celine Mercier 2019-11-29 15:21:08 +01:00
  • 8bc249b2f4 Version 3.0.0-beta1 v3.0.0-beta1 Celine Mercier 2019-09-27 14:52:05 +02:00
  • e308c2e822 versioning 1.0.beta Celine Mercier 2019-09-26 21:05:05 +02:00
  • 3b3cf9359d CMake: unset gcc for nix Celine Mercier 2019-09-26 21:04:42 +02:00
  • be85c55c9e Python: URIs: fixed bug on linux systems Celine Mercier 2019-09-25 14:41:52 +02:00
  • 6d5b904888 Cleaning Celine Mercier 2019-09-25 11:58:00 +02:00
  • 50e8374f6f Added website URL in readme file Celine Mercier 2019-09-25 11:40:00 +02:00
  • 6282242a04 C: Views: fixed a bug when trying to add a comment after changing the file name of a finished view Celine Mercier 2019-09-25 11:39:32 +02:00
  • 44517db51f Fixed gcc warnings Celine Mercier 2019-09-25 11:38:00 +02:00
  • c3b9e46291 more cleaning Celine Mercier 2019-09-24 13:58:53 +02:00
  • 28b7fce59a Cython API: simpler column repr display Celine Mercier 2019-09-22 20:23:31 +02:00
  • fa9555deb9 obi stats: fixed bug with None values Celine Mercier 2019-09-22 20:21:53 +02:00
  • d30f7e7317 more cleaning Celine Mercier 2019-09-22 18:52:05 +02:00
  • 4fa38d9886 cleaning Celine Mercier 2019-09-22 17:38:28 +02:00
  • 71276537a6 obi import: fixed bug when importing a taxdump Celine Mercier 2019-09-22 16:45:30 +02:00
  • ba9ba7aa60 obi grep: now able to convert str to bytes in predicate expressions Celine Mercier 2019-09-22 16:44:45 +02:00
  • 7b4046c288 Bash completion script for commands, dms and views Celine Mercier 2019-09-21 23:46:08 +02:00
  • e2ba76002a Cleaned setup script and put to my name ;) Celine Mercier 2019-09-21 23:44:24 +02:00
  • 336100f716 obi less: now actually behaves like less Celine Mercier 2019-09-21 18:29:12 +02:00
  • d83398c0e0 Cython: View: lines from simple View instances are now displayed in tab instead of dict format Celine Mercier 2019-09-21 18:28:56 +02:00
  • 974d25b815 Cython: Fixed bug in tab formatter with header option always being set to true Celine Mercier 2019-09-21 18:27:47 +02:00
  • ec0737a600 Added signal catching and handling in C and Cython Celine Mercier 2019-09-21 16:47:22 +02:00
  • 06f9d6da60 obi import: importing a view to a DMS now uses the C API (more efficient and imports all metadata) Celine Mercier 2019-09-21 12:49:29 +02:00
  • f0f7edf152 Python API: small option improvements Celine Mercier 2019-09-21 12:08:36 +02:00
  • 9e72c8d16a obi ls: improved taxonomy list Celine Mercier 2019-09-20 20:46:33 +02:00
  • 7c3fa14789 obi import: fixed bug when reading output URI Celine Mercier 2019-09-20 20:43:48 +02:00
  • ec874c095b new command: clean_dms to clean and unlock a DMS after a bad exit. Celine Mercier 2019-09-20 20:38:25 +02:00
  • 783a1343c4 DMS are now locked when used by a command. Added checks and changed cleaning mechanisms. Celine Mercier 2019-09-20 20:37:19 +02:00
  • eb6c59dc1e obi import: proper check for taxonomy name already existing in DMS when importing a taxdump Celine Mercier 2019-09-17 13:41:49 +02:00
  • ad46056179 obi export: if export format is not specified, it is guessed from the view type Celine Mercier 2019-09-17 13:22:41 +02:00
  • 9063e9159d Export options: output option is now only non-positional for obi export Celine Mercier 2019-09-17 13:19:17 +02:00
  • 0159385943 URI decoding: fixed bug with dms-only URI Celine Mercier 2019-09-17 12:50:37 +02:00
  • a0c8deb806 obi export: made output to stdout and pipe in less possible Celine Mercier 2019-09-17 12:31:03 +02:00
  • f566618be6 Added option for no progress bar and made output URI option non positional (for stdout output) Celine Mercier 2019-09-17 12:29:33 +02:00
  • 88451116e8 URIs: added stdout output (empty URI) Celine Mercier 2019-09-17 12:28:10 +02:00
  • eb913b2742 ecotag: trying to use a threshold lower than the ref db threshold now returns an error instead of a warning Celine Mercier 2019-09-15 19:27:47 +02:00
  • f8d1fa678a obi stats: improved display with str instead of bytes Celine Mercier 2019-09-10 16:20:36 +02:00
  • bc55c5ef8c obi clean: fixed an openmp bug where the share size would be 0 blocking the program Celine Mercier 2019-09-10 15:37:33 +02:00
  • f3b0e10c7f fixed a comment Celine Mercier 2019-09-10 14:42:12 +02:00
  • 8f9f2a2d10 obi ls: various improvements Celine Mercier 2019-09-10 14:41:43 +02:00
  • 045a751b0f Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git Celine Mercier 2019-09-05 17:20:13 +02:00
  • ad3a72597f Little fixes for linux compilation Celine Mercier 2019-09-05 17:19:29 +02:00
  • 8899478237 Update README.md Celine Mercier 2019-09-04 17:29:45 +02:00
  • ec614e5d15 Update README.md Celine Mercier 2019-09-04 17:23:30 +02:00
  • f8cccebe19 Update README.md Celine Mercier 2019-09-04 17:11:46 +02:00
  • 5e3c41b058 C: Fixed opened DIR leak Celine Mercier 2019-09-04 16:48:13 +02:00
  • b3a1011d36 C: fixed a bug when opening or creating a new column directory where the DMS was not saved in the struct Celine Mercier 2019-09-04 13:16:28 +02:00
  • a7fabff1c7 C: made it so column DIR* are not kept open to handle very large DMS Celine Mercier 2019-09-04 12:55:21 +02:00
  • f296517716 Various display improvements Celine Mercier 2019-09-03 21:46:39 +02:00
  • d491480af2 C: fixed remaining memory bug in array indexer Celine Mercier 2019-09-01 17:24:57 +02:00
  • 073d98db08 C: ecotag: now prints a warning if the demanded threshold is lower than the db threshold Celine Mercier 2019-08-31 18:30:06 +02:00
  • 0ee728c4d0 C: build_ref_db: now adds a comment with the threshold used to build the DB Celine Mercier 2019-08-31 18:29:40 +02:00
  • 7423bacac0 C: Json comments: added an obi_read_comment function to read one value from comments Celine Mercier 2019-08-31 18:28:51 +02:00
  • 53dcbc8ea3 Fixed log to be in str instead of bytes Celine Mercier 2019-08-29 18:26:51 +02:00
  • 4e75514bad obi import: fixed entry count Celine Mercier 2019-08-29 18:26:09 +02:00
  • 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) Celine Mercier 2019-08-29 17:17:52 +02:00