Eric Coissac
56c1f4180c
Refactor k-mer index management with subcommands and enhanced metadata support
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This commit refactors the k-mer index management tools to use a unified subcommand structure with obik, adds support for per-set metadata and ID management, enhances the k-mer set group builder to support appending to existing groups, and improves command-line option handling with a new global options registration system.
Key changes:
- Introduce obik command with subcommands (index, ls, summary, cp, mv, rm, super, lowmask)
- Add support for per-set metadata and ID management in kmer set groups
- Implement ability to append to existing kmer index groups
- Refactor option parsing to use a global options registration system
- Add new commands for listing, copying, moving, and removing sets
- Enhance low-complexity masking with new options and output formats
- Improve kmer index summary with Jaccard distance matrix support
- Remove deprecated obikindex and obisuperkmer commands
- Update build process to use the new subcommand structure
2026-02-10 06:49:31 +01:00
Eric Coissac
730d448fc3
Allows for only one cpu and it should work
2025-08-06 16:09:25 -04:00
Eric Coissac
6cb7a5a352
Changes to be committed:
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modified: cmd/obitools/obitag/main.go
modified: cmd/obitools/obitaxonomy/main.go
modified: pkg/obiformats/csvtaxdump_read.go
modified: pkg/obiformats/ecopcr_read.go
modified: pkg/obiformats/ncbitaxdump_read.go
modified: pkg/obiformats/ncbitaxdump_readtar.go
modified: pkg/obiformats/newick_write.go
modified: pkg/obiformats/options.go
modified: pkg/obiformats/taxonomy_read.go
modified: pkg/obiformats/universal_read.go
modified: pkg/obiiter/extract_taxonomy.go
modified: pkg/obioptions/options.go
modified: pkg/obioptions/version.go
new file: pkg/obiphylo/tree.go
modified: pkg/obiseq/biosequenceslice.go
modified: pkg/obiseq/taxonomy_methods.go
modified: pkg/obitax/taxonomy.go
modified: pkg/obitax/taxonset.go
modified: pkg/obitools/obiconvert/sequence_reader.go
modified: pkg/obitools/obitag/obitag.go
modified: pkg/obitools/obitaxonomy/obitaxonomy.go
modified: pkg/obitools/obitaxonomy/options.go
deleted: sample/.DS_Store
2025-06-04 09:48:10 +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
8448783499
Make sequence files recognized as a taxonomy
2025-03-14 14:22:22 +01:00
Eric Coissac
d1c31c54de
add a first version of the inline documentation
2025-03-12 14:40:42 +01:00
Eric Coissac
78caabd2fd
Add basic test on -h for all the commands
2025-03-08 16:28:06 +01:00
Eric Coissac
b18c9b7ac6
add the --raw-taxid option
2025-03-08 09:40:06 +01:00
Eric Coissac
6a8061cc4f
Add managment of the taxonomy alias politic
2025-02-10 14:05:47 +01:00
Eric Coissac
2452aef7a9
patch multiple -Z options
2025-01-29 21:35:28 +01:00
Eric Coissac
7c4042df6b
introduce obidefault
2025-01-27 17:12:45 +01:00
Eric Coissac
9acb4a85a8
Refactoring of the default values
2025-01-24 18:09:59 +01:00
Eric Coissac
3137c1f841
Adds the ability to read gzip-tar file for the taxonomy dump
2025-01-24 11:47:59 +01:00
Eric Coissac
ccd3b06532
Merge branch 'master' into taxonomy
2024-12-20 20:06:57 +01:00
Eric Coissac
40fb4e9767
reduce the memory impact of obiuniq.
2024-11-27 13:30:16 +01:00
Eric Coissac
f3d8707c08
Add default taxonomy
2024-11-16 10:01:07 +01:00
Eric Coissac
373464cb06
On development genome skim tools
2024-08-30 11:17:33 +02:00
Eric Coissac
e40d0bfbe7
Debug fasta and fastq writer when the first sequence is hudge
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Former-commit-id: d208ff838abb7e19e117067f6243298492d60f14
2024-06-26 18:39:42 +02:00
Eric Coissac
e6b87ecd02
Reduce memory allocation events
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Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
2024-06-22 21:01:53 +02:00
Eric Coissac
411124d1b3
Add automatic rules to manage version number
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Former-commit-id: f4fcc1927f4169025c1d8cc88c5f3abcdc76037c
2024-06-01 17:26:16 +02:00
Eric Coissac
4487723d14
Adds possibility to provide the ngsfilter configuration as a CSV file
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Former-commit-id: f0fd2cb1a7b149ae2a330edc5087b21be2c4585b
2024-05-31 11:08:20 +02:00
Eric Coissac
55ce36f329
Update of obipcr and homogenization of logging
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Former-commit-id: 46abf47c19ace5248042c02cf1f81d9f6c12eb10
2024-05-16 15:18:30 +02:00
Eric Coissac
5b98393a68
Refactor sequence file reading
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Former-commit-id: 3dcb96e68da648d72bb585da047e3496427d7851
2024-05-01 00:50:23 +02:00
Eric Coissac
33d4d63acd
Adds a warning on max-cpu = 1
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Former-commit-id: ed02328d7d0e36b7c6b77ea776c0bde7c0eb64f3
2024-04-30 13:27:19 +02:00
Eric Coissac
cb35612a6c
new --version option and qualities method in obiscript
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Former-commit-id: 7b0ce2901785d5c7494dec3a7a95d1fc5dc4a52b
2024-04-13 12:40:43 +02:00
61c30f9b6a
Patch rev complement and first implementation of --auto in obicsv
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Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
2023-11-07 09:37:07 +02:00
d46f6b06c5
several small changes
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Former-commit-id: c1cdb95885e44fd6ee7d1c963860d7ab41230c96
2023-06-07 17:50:10 +02:00
d70bb45f3f
Small change in parallelisation tuning
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Former-commit-id: 3fe2495b7fd86a0ba47dd87907323a457bae481a
2023-04-05 14:15:47 +02:00
84b3e4d097
Reduce memomry inprint of obipcr
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Former-commit-id: bd25be2d454f083c729346a828e27f07ad1a216e
2023-03-31 10:53:53 +02:00
e863dc456a
Add an option --pprof
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Former-commit-id: 3ca1280e8daddbf1075e3189f9851211ce8882ae
2023-03-28 20:07:26 +07:00
7ed567fbad
Make the --help or -h options working when mandatory options are declared
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Former-commit-id: db502ff81dcf20449d126978fcebf890edb814ae
2023-03-21 22:01:20 +07:00
d88de15cdc
Refactoring codes for removing buffer size options. An some other changes...
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Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
2023-03-07 11:12:13 +07:00
072b85e155
change the model for representing paired reads and extend its usage to other commands
2023-02-23 23:35:58 +01:00
abcf02e488
Start to use leveled log
2022-02-24 12:14:52 +01:00
38e4655f38
Correct for a strange bug...
2022-02-07 11:51:35 +01:00
30d80db02d
All an option to limit number of CPU
2022-02-06 18:52:53 +01:00
8dbda68746
Adds the command obimultiplex
2022-02-01 17:31:28 +01:00
e8fff6477b
Work on iterators and recycling of biosequences
2022-01-14 23:11:36 +01:00
ff40222902
Code reefactoring
2022-01-14 16:10:19 +01:00
f53bf1b804
First commit
2022-01-13 23:27:39 +01:00
