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46 Commits

Author SHA1 Message Date
Eric Coissac
b26b76cbf8 Add TOML persistence support for KmerSet and KmerSetGroup 
This commit adds support for saving and loading KmerSet and KmerSetGroup structures using TOML, YAML, and JSON formats for metadata. It includes:

- Added github.com/pelletier/go-toml/v2 dependency
- Implemented Save and Load methods for KmerSet and KmerSetGroup
- Added metadata persistence with support for multiple formats (TOML, YAML, JSON)
- Added helper functions for format detection and metadata handling
- Updated version commit hash
 2026-02-05 14:57:22 +01:00
Eric Coissac
28162ac36f Ajout du filtre de fréquence avec v niveaux Roaring Bitmaps 
Implémentation complète du filtre de fréquence utilisant v niveaux de Roaring Bitmaps pour éliminer efficacement les erreurs de séquençage.

- Ajout de la logique de filtrage par fréquence avec v niveaux
- Intégration des bibliothèques RoaringBitmap et bitset
- Ajout d'exemples d'utilisation et de documentation
- Implémentation de l'itérateur de k-mers pour une utilisation mémoire efficace
- Optimisation pour les distributions skewed typiques du séquençage

Ce changement permet de filtrer les k-mers par fréquence minimale avec une utilisation mémoire optimale et une seule passe sur les données.
 2026-02-04 21:21:10 +01:00
Eric Coissac
c2f38e737b Update of the packages 2025-04-10 15:16:36 +02:00
Eric Coissac
8671285d02 add the --min-sample-count option to obiclean. 2025-02-24 08:48:31 +01:00
Eric Coissac
773e54965d Patch a bug on compressed output 2025-02-05 14:18:24 +01:00
Eric Coissac
b9bee5f426 Changes to be committed: 
modified:   go.mod
	modified:   go.sum
	modified:   pkg/obilua/obilib.go
	modified:   pkg/obilua/obiseq.go
	modified:   pkg/obilua/obiseqslice.go
	new file:   pkg/obilua/obitaxon.go
	new file:   pkg/obilua/obitaxonomy.go
	modified:   pkg/obioptions/version.go
 2025-02-02 16:52:52 +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
3d06978808 a functional new version of obifind 2024-11-24 19:33:24 +01:00
Eric Coissac
9e8a7fd9be Patch a bug in fastq reader 2024-10-20 16:07:43 +02:00
Eric Coissac
b37fc39ead switch to go version 1.23.1 2024-09-24 15:55:01 +02:00
Eric Coissac
bdb96dda94 Adds the obimicrosat command 2024-08-05 15:31:20 +02:00
Eric Coissac
c7ed47e110 first version of obidemerge, obijoin and a new filter for obicleandb but to be finnished 
Former-commit-id: 8a1ed26e5548c30db75644c294d478ec4d753f19
 2024-07-10 15:21:42 +02:00
Eric Coissac
c1f03cb1f6 Switch to faster json library go-json and sonic 
Former-commit-id: ab9b4723f1dcf79fe5c073fff4d86f4f6969edfd
 2024-06-23 00:36:08 +02:00
Eric Coissac
411124d1b3 Add automatic rules to manage version number 
Former-commit-id: f4fcc1927f4169025c1d8cc88c5f3abcdc76037c
 2024-06-01 17:26:16 +02:00
Eric Coissac
d249902073 A lot of changes and debug... A complete first 
version of the recipy in the Cookbook about
avaluating primers


Former-commit-id: 6c816f5546b3f472f6930d112abe3da04d2d5a55
 2024-05-26 12:56:29 +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
e25c3b7365 Bug in the json parsing 
Former-commit-id: e652b04b9fa7e11124eb5930c7bec4613c808758
 2024-03-19 13:50:13 +01:00
Eric Coissac
b40015deb7 first preliminary version of obiscript. 
Former-commit-id: 0d2c0fc5e33e0873ba5c04aca4cf7dd69aa83c90
 2024-03-06 12:56:44 -03:00
Eric Coissac
38c49e9f38 Switch GOPATH to the local directory in Makefile 
Former-commit-id: ae00f1136021e6fcd5047aadb4762653cf003d5d
 2024-02-27 07:22:57 +01:00
Eric Coissac
95caebec8f update modules 
Former-commit-id: 04651744d21f0db3406a0aa7bb9cdf9729140349
 2024-02-16 18:12:59 +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
9ee45701b7 correction of two warnings 
Former-commit-id: d2d08b5d6f7511598625536f5a708db347742c20
 2023-11-09 22:37:55 +02:00
Eric Coissac
a96ecb4837 Adds some unit test 
Former-commit-id: b1a59df1c87187a1538f30c447d42bbe96402419
 2023-11-08 11:13:56 +02:00
Eric Coissac
dedf125f6e Patch a bug in Subsequence and adds few unit tests. 
Former-commit-id: caddc9ad6523e4ef02899bfe83cc8681ef674383
 2023-11-08 10:16:34 +02:00
Eric Coissac
61c30f9b6a Patch rev complement and first implementation of --auto in obicsv 
Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
 2023-11-07 09:37:07 +02:00
Eric Coissac
62b57f4ede A go implementation of the fasta reader 
Former-commit-id: 603592c4761fb0722e9e0501d78de1bd3ba238fa
 2023-09-01 09:30:12 +02:00
Eric Coissac
45ea4dacf7 Every small changes to include into Release 4.0.4 
Former-commit-id: b2a48c5b5c471f072785e02d4bb0f149a09cdf6f
 2023-08-27 17:22:51 +02:00
Eric Coissac
be47ec909c add the --skip-empty option 
Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5
 2023-07-17 14:24:02 +02:00
Eric Coissac
f6628a1ba2 Update install script 
Former-commit-id: 0dc6b22490fe6228e0099bd96fb1c53ee2754f03
 2023-05-23 10:09:42 +02:00
Eric Coissac
0746c95f4f Update the package dependencies 
Former-commit-id: e3fecfd65ec03f3a354338f16c52c130ea25c7f9
 2023-03-28 21:30:25 +07:00
Eric Coissac
98eac2360c adds a rule to update packages and push the corresponding updates module files 
Former-commit-id: 1ffa805e74571f9d970dcb185f187dd586c1a190
 2023-03-21 22:02:18 +07:00
Eric Coissac
b3922c3896 Produce less weird crash on non existing files 
Former-commit-id: 74bb27bd53c685be530632994bd2ba24c1f362e1
 2023-03-07 17:34:25 +07:00
Eric Coissac
d4b185b716 Adds some new dependencies 
Former-commit-id: 2f31ea6f852651e1ffca1d9ce78b17bddd26f2bb
 2023-03-07 11:12:39 +07:00
Eric Coissac
6c5fc8f65b Save change in various files 
Former-commit-id: 428f8ee77c584b79cc2ef45eef2902c3e0754c77
 2023-02-23 23:45:41 +01:00
Eric Coissac
08521c74e2 Adds Aho-Corasick matching to obiannotate 2023-02-09 15:59:11 +01:00
Eric Coissac
18be4becec Add some new packages 2022-11-14 14:36:04 +01:00
Eric Coissac
aae3398701 Replace the CopyMap function by the MustFillMap and adds a InterfaceToIntMap function 2022-10-12 22:56:38 +02:00
Eric Coissac
91c2ce551d Add new modules 2022-08-23 15:09:03 +02:00
Eric Coissac
5dd835d3e7 A first functional version of obiclean 2022-08-20 18:01:07 +02:00
Eric Coissac
0a36447e2a Adds the log module 2022-02-24 12:15:36 +01:00
Eric Coissac
f18cc034bb add an option alias -O for the old obi format 2022-02-24 07:26:55 +01:00
Eric Coissac
eb32620bb3 Adds a first version of a new obidistribute command 2022-02-14 00:01:01 +01:00
Eric Coissac
1544bafde1 Updates modules 2022-02-09 22:03:38 +01:00
Eric Coissac
79fcd98e43 updated go.mod 2022-02-07 11:52:06 +01:00
Eric Coissac
e1b7e1761c Change the memory management for thee BuildAlignment function 2022-01-15 19:10:16 +01:00
Eric Coissac
b9b9c0f179 Patch module name from oa2 to obitools 2022-01-13 23:43:01 +01:00