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  • 3db93ee9c4 Fixed stdout output master v3.0.1b256 Celine Mercier 2024-01-12 16:13:30 +13:00
  • 4844b20770 Merge branch 'master' of https://git.metabarcoding.org/obitools/obitools3 Celine Mercier 2024-01-12 15:36:58 +13:00
  • 0d98a4f717 Switch to version 3.0.1b26 Celine Mercier 2024-01-10 16:40:08 +13:00
  • 837ff1a1ba Taxonomy: fixed an issue related to StopIteration behaviour in new versions of python Celine Mercier 2024-01-10 15:53:15 +13:00
  • aeed42456a export: columns are now in alphabetical order when exporting to tab format Celine Mercier 2024-01-10 15:52:28 +13:00
  • 6819d04615 Testing RAM instead of mmap for blob alignment adria_build_ref_db Celine Mercier 2023-11-29 16:24:31 +13:00
  • fb6e27bb5d Revert "Testing RAM instead of mmap for blob alignment" Celine Mercier 2023-11-29 04:22:31 +01:00
  • 6d94cdcc0d Testing RAM instead of mmap for blob alignment Celine Mercier 2023-11-29 16:19:34 +13:00
  • 8a1f844645 obi import: fixed bug caused by new behaviour of StopIteration exceptions in Python>=3.7 v3.0.1b25 Celine Mercier 2023-09-21 17:47:40 +12:00
  • 791ccfb92e Fixed include bug in previous version and switch to version 3.0.1b24 v3.0.1b24 Celine Mercier 2023-05-15 11:35:42 +12:00
  • 1c9a906f5b ngsfilter and ecopcr: now check for primers too long for apat library to handle (31bp max) and switch to version 3.0.1b23 Celine Mercier 2023-05-12 17:04:21 +12:00
  • 55b2679b23 New command obi rm and switch to version 3.0.1b22 v3.0.1b22 Celine Mercier 2023-05-08 17:48:50 +12:00
  • 9ea2124adc Switch to version 3.0.1b21 v3.0.1b21 Celine Mercier 2023-02-13 11:00:01 +13:00
  • 2130a949c7 New command: obi taxonomy to add local taxa (closes #64) Celine Mercier 2023-02-13 10:59:20 +13:00
  • eeb93afa7d import: now automatically renames scientific_name tag to SCIENTIFIC_NAME, and suggests using --input-na-string when a sequence import fails Celine Mercier 2023-02-13 10:40:38 +13:00
  • 755ce179ad head: added output format options Celine Mercier 2023-02-13 10:31:26 +13:00
  • 7e492578b3 Switch to version 3.0.1b20 v3.0.1b20 Celine Mercier 2022-09-21 11:33:03 +12:00
  • 02e9df3ad1 alignpairedend and ngsfilter: ids of original sequences are now kept Celine Mercier 2022-09-21 11:32:19 +12:00
  • 55ada80500 import: made ngsfilter file parsing more resilient and switching to version 3.0.1b19 v3.0.1b19 mercierc 2022-07-15 16:02:21 +12:00
  • ef9d9674b0 obi import: added SINTAX format import and switch to version 3.0.1b18 v3.0.1b18 mercierc 2022-05-17 09:36:33 +12:00
  • 4f39bb2418 switch to version 3.0.1b17 v3.0.1b17 mercierc 2022-05-03 10:55:36 +12:00
  • 0a2b8adb50 import: added import of UNITE fasta format mercierc 2022-05-03 10:54:41 +12:00
  • f9b99a9397 annotate: fixed a bug where a column type could be wrongly guessed and switch to version 3.0.1b16 v3.0.1b16 mercierc 2022-03-30 16:32:07 +13:00
  • ce2833c04b switch to version v3.0.1b15 v3.0.1b15 Celine Mercier 2022-02-25 17:48:44 +13:00
  • f64b3da30b split command Celine Mercier 2022-02-25 17:44:18 +13:00
  • 388b3e0410 removed a trace v3.0.1b14 mercierc 2021-11-11 15:53:27 +13:00
  • c9db990b83 switch to version 3.0.1b14 mercierc 2021-11-11 15:28:00 +13:00
  • 3f253feb5e Cython: View: fixed keys method to get list of view keys mercierc 2021-11-11 15:27:32 +13:00
  • 85d2bab607 small fix mercierc 2021-11-11 15:26:48 +13:00
  • 53b3d81137 small fixes and improvements mercierc 2021-11-11 15:26:09 +13:00
  • f6353fbf28 obi export: added options to export to metabaR compatible format mercierc 2021-11-11 15:24:12 +13:00
  • 5a8b9dca5d goes with previous commit mercierc 2021-11-11 15:12:04 +13:00
  • 8bd6d6c8e9 Python: URI decoding: now properly checking that paths can be encoded in ASCII (issue #89) mercierc 2021-11-02 11:17:59 +13:00
  • 405e6ef420 Python: URI decoding: added metabaR output mercierc 2021-11-02 11:16:29 +13:00
  • fedacfafe7 switch to version 3.0.1b13 v3.0.1b13 mercierc 2021-09-13 11:46:17 +12:00
  • 2d66e0e965 python: genbank parser: better handling of white spaces mercierc 2021-09-13 11:44:38 +12:00
  • f43856b712 switch to version 3.0.1b12 v3.0.1b12 mercierc 2021-09-08 10:56:55 +12:00
  • 9e0c319806 Cython: fixed rewriting of column when rewriting a 1 element dict column mercierc 2021-09-08 10:54:23 +12:00
  • 58b42cd977 C: views: now correctly parses view names containing '.' when cleaning unfinished views. Closes #115 mercierc 2021-09-08 10:52:42 +12:00
  • 34de90bce6 ngsfilter: checks better if there is an associated sequencing quality mercierc 2021-09-08 10:30:11 +12:00
  • 4be9f36f99 stats: fixed the computation of variance when it is equal to 0 mercierc 2021-08-05 11:32:16 +12:00
  • f10e78ba3c C: fixed the printing of view informations from a DMS (fixes #114) mercierc 2021-08-05 11:31:24 +12:00
  • 88c8463ed7 Cython: taxonomy: improved logging mercierc 2021-08-05 11:29:20 +12:00
  • 89168271ef ecopcr: now accepting taxonomy from a different DMS than the reference sequences mercierc 2021-08-05 11:28:57 +12:00
  • 82d2642000 Switch to version 3.0.1b11 v3.0.1b11 mercierc 2021-07-22 09:25:39 +12:00
  • 99c1cd60d6 export: now exports header for tabular files by default and added option to only export specific columns mercierc 2021-07-22 09:23:18 +12:00
  • ce7ae4ac55 export: fixed 'only' option printing one too many if printing header mercierc 2021-07-21 15:23:04 +12:00
  • 0b4283bb58 cat: improved error handling mercierc 2021-07-21 15:22:08 +12:00
  • 747f3efbb2 Improved taxonomy reading information display mercierc 2021-07-21 15:20:44 +12:00
  • 6c1a3aff47 Fixed the handling of sample names that are numbers (forcing conversion) mercierc 2021-07-21 15:19:24 +12:00
  • e2932b05f2 Implements #108 export integer missing values as 0 for tables by default mercierc 2021-07-21 14:41:54 +12:00
  • 32345b9ec4 Addresses #111 mercierc 2021-07-19 15:55:25 +12:00
  • 9334cf6cc6 import: improved genbank parser and switch to version 3.0.1.b10 v3.0.1b10 mercierc 2021-06-17 08:42:01 +12:00
  • 8ec13a294c Switch to version 3.0.1b9 v3.0.1b9 mercierc 2021-06-01 09:21:43 +12:00
  • 3e45c34491 import: now imports and adds taxids for SILVA and RDP files, added import of lists, fixed skipping of errors (was not overwriting), and fixed --no-progress-bar option mercierc 2021-06-01 09:21:07 +12:00
  • c2f3d90dc1 build_ref_db: set default threshold to 0.99 mercierc 2021-06-01 09:11:17 +12:00
  • 6b732d11d3 align: fixed column URI parsing mercierc 2021-06-01 09:10:21 +12:00
  • 9eb833a0af typo fix mercierc 2021-06-01 09:09:16 +12:00
  • 6b7b0e3bd1 cat: fixed the handling of dictionary columns mercierc 2021-06-01 09:06:13 +12:00
  • 47691a8f58 count: added option to specify the count column mercierc 2021-06-01 09:05:14 +12:00
  • b908b581c8 clean: hid not implemented option mercierc 2021-06-01 09:04:22 +12:00
  • 03c174fd7a grep: added taxonomy check mercierc 2021-05-31 17:03:39 +12:00
  • 2156588ff6 added TODO comment mercierc 2021-05-31 17:01:57 +12:00
  • 6ff29c6a6a Increased maximum line count to 10E12 mercierc 2021-05-31 17:00:55 +12:00
  • 51a3c68fb5 C: build_reference_db: fixed gcc warning/error mercierc 2021-05-31 16:59:17 +12:00
  • da91ffc2c7 URI decoding: fixed reading a taxonomy before any view mercierc 2021-05-31 16:57:20 +12:00
  • c884615522 obi stats: various fixes and improvements mercierc 2021-05-31 16:51:06 +12:00
  • cb53381863 ecotag: BEST_MATCH_TAXIDS now dereplicated (no repeated taxids in the list) and switch to version 3.0.1b8 v3.0.1b8 mercierc 2021-05-10 16:02:06 +12:00
  • 72b3e5d872 switch to version 3.0.1b7 v3.0.1b7 MercierC 2021-04-07 10:31:54 +12:00
  • 238e9f70f3 alignpairedend: fixed bug that would cut out sequence ends when it should not have MercierC 2021-04-07 10:31:12 +12:00
  • e099a16624 small fixes MercierC 2021-04-07 10:28:02 +12:00
  • 847c9c816d import: fixed count estimation for tabular files with header MercierC 2021-03-30 09:07:14 +13:00
  • 6026129ca8 Fixes 101 MercierC 2021-03-30 09:06:08 +13:00
  • 169b6514b4 small doc fixes MercierC 2021-03-29 13:07:48 +13:00
  • 89b0c48141 switch to version 3.0.1b6 v3.0.1b6 MercierC 2021-03-29 11:18:44 +13:00
  • 7c02782e3c import/export: workaround for issue where flake8(?) reads '\t' as '\'+'t' when parsing an option value MercierC 2021-03-29 11:18:19 +13:00
  • ecc4c2c78b stats: improved the tabular display MercierC 2021-03-29 09:03:32 +13:00
  • f5413381fd C: taxonomy: fixed a bug where some taxa would not be stored in the merged index MercierC 2021-03-29 09:02:18 +13:00
  • 3e93cfff7b import: Columns are now rewritten in OBI_FLOAT if a value is > INT32_MAX MercierC 2021-03-29 09:00:52 +13:00
  • 6d445fe3ad switch to version 3.0.1b5 v3.0.1b5 MercierC 2021-03-22 09:41:01 +13:00
  • 824deb7e21 new command: obi rm: deletes any view (for now the user deleting a view accepts that there will be missing information when running obi history if other views came from the deleted view) MercierC 2021-03-18 09:17:06 +13:00
  • d579bb2749 switch to version 3.0.1b4 v3.0.1b4 MercierC 2021-03-16 17:40:58 +13:00
  • 10e5ebdbc0 ngsfilter: fixed critical bug where barcodes shorter than the forward primer would be missed MercierC 2021-03-16 15:09:28 +13:00
  • 8833110490 import: fixed the import of tabular files with no header MercierC 2021-03-16 09:15:48 +13:00
  • bd38449f2d switch to version 3.0.1b3 v3.0.1b3 MercierC 2021-03-15 16:50:17 +13:00
  • 904823c827 uniq: now OK to use -m option even if only one unique key in information to merge (e.g. one sample) MercierC 2021-03-15 16:48:22 +13:00
  • af68a1024c Switch to version 3.0.1b2 v3.0.1b2 MercierC 2021-03-15 16:26:43 +13:00
  • 425fe25bd2 Made the OBITools3 more 'empty file friendly' MercierC 2021-03-15 16:25:41 +13:00
  • d48aed38d4 switch to version 3.0.1b1 v3.0.1b1 Celine Mercier 2021-03-11 17:11:23 +13:00
  • 5e32f8523e Merge branch 'wsl_version' Celine Mercier 2021-03-11 16:47:59 +13:00
  • 8f1d94fd24 obi test: fixed bug introduced in ad1fd3c3 wsl_version Celine Mercier 2021-03-11 16:31:31 +13:00
  • 38f42cb0fb C: Made maximum file path length 2048 instead of 1024 MercierC 2021-03-11 15:23:22 +13:00
  • 7f0f63cf26 C: now completely unmapping files before truncating them to a smaller size (#68) MercierC 2021-03-11 15:12:40 +13:00
  • cba78111c9 obi test: fixed bug introduced in previous version Celine Mercier 2021-03-11 11:36:52 +13:00
  • 41fbae7b6c Switch to version 3.0.0b43 v3.0.0b43 Celine Mercier 2021-03-10 16:52:03 +13:00
  • ad1fd3c341 Now handling dictionaries with one key Celine Mercier 2021-03-10 16:50:30 +13:00
  • fbf0f7dfb6 import: improved genbank parser and switch to version 3.0.0b42 v3.0.0b42 Celine Mercier 2021-02-17 15:26:35 +13:00
  • fda0edd0d8 Switch to version 3.0.0b41 v3.0.0b41 Celine Mercier 2021-02-10 17:29:08 +13:00
  • 382e37a6ae Fixes #88 Celine Mercier 2021-02-10 17:28:49 +13:00
  • 5cc3e29f75 obi test: made less heavy by default Celine Mercier 2021-02-10 17:28:15 +13:00