25 Commits

Author	SHA1	Message	Date
Eric Coissac	c188580aac	Replace Rebatch with RebatchBySize using default batch parameters ... Replace calls to Rebatch(size) with RebatchBySize(obidefault.BatchMem(), obidefault.BatchSizeMax()) in batchiterator.go, fragment.go, and obirefidx.go to ensure consistent use of default memory and size limits for batch rebatching.	2026-03-13 15:16:33 +01:00
Eric Coissac	1a28d5ed64	Add progress bar configuration and conditional display ... This commit introduces a new configuration module `obidefault` to manage progress bar settings, allowing users to disable progress bars via a `--no-progressbar` option. It updates various packages to conditionally display progress bars based on this new configuration, improving user experience by providing control over progress bar output. The changes also include improvements to progress bar handling in several packages, ensuring they are only displayed when appropriate (e.g., when stderr is a terminal and stdout is not piped).	2026-02-08 16:14:02 +01:00
Eric Coissac	d31e677304	Patch a bug in obitag	2025-06-04 14:47:28 +02:00
Eric Coissac	5a3705b6bb	Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.	2025-03-25 16:44:46 +01:00
Eric Coissac	7c4042df6b	introduce obidefault	2025-01-27 17:12:45 +01:00
Eric Coissac	5d0f996625	Patch a small bug on json write	2024-12-20 19:42:03 +01:00
Eric Coissac	795df34d1a	Changes to be committed: ... modified: cmd/obitools/obitag/main.go modified: cmd/obitools/obitag2/main.go modified: go.mod modified: go.sum modified: pkg/obiformats/ncbitaxdump/read.go modified: pkg/obioptions/version.go modified: pkg/obiseq/attributes.go modified: pkg/obiseq/taxonomy_lca.go modified: pkg/obiseq/taxonomy_methods.go modified: pkg/obiseq/taxonomy_predicate.go modified: pkg/obitax/inner.go modified: pkg/obitax/lca.go new file: pkg/obitax/taxid.go modified: pkg/obitax/taxon.go modified: pkg/obitax/taxonomy.go modified: pkg/obitax/taxonslice.go modified: pkg/obitools/obicleandb/obicleandb.go modified: pkg/obitools/obigrep/options.go modified: pkg/obitools/obilandmark/obilandmark.go modified: pkg/obitools/obilandmark/options.go modified: pkg/obitools/obirefidx/famlilyindexing.go modified: pkg/obitools/obirefidx/geomindexing.go modified: pkg/obitools/obirefidx/obirefidx.go modified: pkg/obitools/obirefidx/options.go modified: pkg/obitools/obitag/obigeomtag.go modified: pkg/obitools/obitag/obitag.go modified: pkg/obitools/obitag/options.go modified: pkg/obiutils/strings.go	2024-12-19 13:36:59 +01:00
Eric Coissac	1b1cd41fd3	Add some code refactoring from the blackboard branch	2024-08-02 12:35:46 +02:00
Eric Coissac	dd9307a4cd	Swich to the system min and max functions and remove the version from obiutils ... Former-commit-id: 8c4558921b0d0c266b070f16e83813de6e6d4a0f	2024-05-30 08:27:24 +02:00
Eric Coissac	55ce36f329	Update of obipcr and homogenization of logging ... Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10	2024-05-16 15:18:30 +02:00
Eric Coissac	017030bcce	Add obiminion first version ... Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d	2024-05-14 08:16:12 +02:00
Eric Coissac	b9a7961c91	Add more error checks on taxonomy reading ... Former-commit-id: 30c848d8e61214afcc7d92f0d3a3f5a1474fc720	2023-12-14 08:09:06 +01:00
Eric Coissac	8d77cc4133	Change path of the obitools pkg ... Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65	2023-11-29 12:14:37 +01:00
Eric Coissac	9bf006af93	A first prototype for the space of sequences ... Former-commit-id: 07dc6ef044b5b6a6fb45dc2acb01dffe71a96195	2023-08-27 14:58:55 +02:00
Eric Coissac	7f08f58336	several correction in obitag and adds the --save-db option ... Former-commit-id: b3a15b1a1b3971388a8749faaba519028f6e976c	2023-06-07 17:45:11 +02:00
Eric Coissac	e9574bae07	Small change to increase efficiency (a little) ... Former-commit-id: fa54c9bf82b8ba60653255ab2a5f671619dcfdcb	2023-05-05 13:33:15 +02:00
Eric Coissac	3778ae9266	Correction a a bug and transfert of the new matching rules from obirefidx to obitag ... Former-commit-id: a28540f72a504ad4e7e8a8b6f7609116913445b4	2023-05-05 07:37:19 +02:00
Eric Coissac	88a9e38952	Took better advantage of taxonomy structure and LCA upperbound base on common word. Accelleration by a factor two of obirefidx compared to previous version. ... Former-commit-id: 35f40498d642058e9dbff20128d11303a314018d	2023-05-04 09:32:47 +02:00
Eric Coissac	870cb1aabb	New refdb indexing algorithm ... Former-commit-id: 7ae480cec5d277a08620a2e666b5c9b69bb6cd73	2023-05-03 15:32:31 +02:00
Eric Coissac	d5e84ec676	rename goutils to obiutils ... Former-commit-id: 2147f53db972bba571dfdae30c51b62d3e69cec5	2023-03-24 10:25:12 +07:00
Eric Coissac	f97f92df72	rename the iterator class	2023-01-22 22:04:17 +01:00
Eric Coissac	f674200a6e	FastLCS with maxError=-1 is equivalent to FullLCS.	2022-11-16 09:57:36 +01:00
Eric Coissac	4375dbd9bb	Switxh alignment to the new LCS method and make a copy of the sequences before annotating them to prevent concurrent map access bug	2022-11-16 09:27:04 +01:00
Eric Coissac	f3ddac0f50	Small adjustment	2022-10-27 11:18:44 +02:00
Eric Coissac	8aa323dad5	Add a first version of obitag the successor of ecotag	2022-10-26 13:16:56 +02:00