Eric Coissac
7a979ba77f
Add obisuperkmer command implementation and tests
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This commit adds the implementation of the obisuperkmer command, including:
- The main command in cmd/obitools/obisuperkmer/
- The package implementation in pkg/obitools/obisuperkmer/
- Automated tests in obitests/obitools/obisuperkmer/
- Documentation for the implementation and tests
The obisuperkmer command extracts super k-mers from DNA sequences, following the standard OBITools architecture. It includes proper CLI option handling, validation of parameters, and integration with the OBITools pipeline system.
Tests cover basic functionality, parameter validation, output format, metadata preservation, and file I/O operations.
2026-02-07 13:54:02 +01:00
Eric Coissac
4603d7973e
implementation de obilowmask
2025-11-18 15:30:20 +01:00
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
c0ecaf90ab
Add the --number option to obiannotate
2025-04-22 18:35:51 +02:00
Eric Coissac
7542e33010
Several bugs dicoverd during the doc writing
2025-04-04 16:59:27 +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
2ab6f67d58
Add a progress bar to chimera detection
2025-03-25 08:37:27 +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
65bd29b955
normalize the usage of obitaxonomy
2025-03-08 13:00:55 +01:00
Eric Coissac
6a8061cc4f
Add managment of the taxonomy alias politic
2025-02-10 14:05:47 +01:00
Eric Coissac
d3dac1b21f
Make obitag able to use the taxonomic path included in reference database as taxonomy
2025-01-30 11:50:03 +01:00
Eric Coissac
0df082da06
Adds possibility to extract a taxonomy from taxonomic path included in sequence files
2025-01-30 11:18:21 +01:00
Eric Coissac
8a28c9ae7c
add the --download-ncbi option to obitaxonomy
2025-01-29 12:38:39 +01:00
Eric Coissac
00f2dc2697
Rename obifind obitaxonomy and introduce the new CSV format for taxonomy.
2025-01-29 10:45:26 +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
ffd67252c3
patch a bug in obimultiplex: change option -t into -s
2025-01-23 13:50:24 +01:00
Eric Coissac
d066bb6878
Changes to be committed:
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modified: .gitignore
modified: cmd/test/main.go
modified: pkg/obioptions/version.go
2025-01-09 07:24:41 +01:00
Eric Coissac
67c0d00a4d
remove the obitag2 command
2025-01-07 11:50:28 +01:00
Eric Coissac
ccd3b06532
Merge branch 'master' into taxonomy
2024-12-20 20:06:57 +01:00
Eric Coissac
795df34d1a
Changes to be committed:
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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
ad2461a656
some minor improvements
2024-11-27 13:36:06 +01:00
Eric Coissac
40fb4e9767
reduce the memory impact of obiuniq.
2024-11-27 13:30:16 +01:00
Eric Coissac
3d06978808
a functional new version of obifind
2024-11-24 19:33:24 +01:00
Eric Coissac
f3d8707c08
Add default taxonomy
2024-11-16 10:01:07 +01:00
Eric Coissac
03f4e88a17
Fisrt functional version
2024-11-14 19:10:23 +01:00
Eric Coissac
7255c71576
commit version
2024-09-24 16:36:59 +02:00
Eric Coissac
373464cb06
On development genome skim tools
2024-08-30 11:17:33 +02:00
Eric Coissac
31bfc88eb9
Patch a bug on writing to stdout, and add clearer error on openning data files
2024-08-13 09:45:28 +02:00
Eric Coissac
bdb96dda94
Adds the obimicrosat command
2024-08-05 15:31:20 +02:00
Eric Coissac
1b1cd41fd3
Add some code refactoring from the blackboard branch
2024-08-02 12:35:46 +02:00
Eric Coissac
2247c3bc0a
obitag xprize version
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Former-commit-id: 2c47d88724102b115aac5641abccb880dfbec64d
2024-07-25 18:11:11 -04:00
Eric Coissac
4e4fac491f
Fisrt versin of the two levels indexing
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Former-commit-id: 4d86483bc120e27cb6f5d2c216596d410274fc69
2024-07-12 15:17:48 +02:00
Eric Coissac
42c5881ddc
some cleanning on the new tools
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Former-commit-id: f265a3910d2872c56af81c9b873669f2cb627781
2024-07-11 10:46:11 +02:00
Eric Coissac
154753de90
Same bug but for fastq sequence writing only
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Former-commit-id: 86d208fe66828da9943c559df80ff095b07eaf7a
2024-06-26 18:46:47 +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
3a7661f324
obimultiplex2 in now obimultiplex
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Former-commit-id: ee6f5e15a3f1729dfc2806d039c842c9c3bdd343
2024-06-07 09:04:37 +02:00
Eric Coissac
a0a9fb461c
trial on rewriting obimultiplex
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Former-commit-id: d00f3353d83760dc878c6411ad344d96216096a7
2024-06-04 16:50:07 +02:00
Eric Coissac
38945d0a41
Adds the --template option to obimultiplex
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Former-commit-id: 349e9f278abd6a6c258f31d99ea04853a79c62de
2024-05-31 11:34:06 +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
61be8a55b1
Merge obiminion and obiconsensus
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Former-commit-id: 49d65d671e9fe4454de60c20507c3d8df6e9c51c
2024-05-14 17:53:32 +02:00
Eric Coissac
017030bcce
Add obiminion first version
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Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
2024-05-14 08:16:12 +02:00
b40015deb7
first preliminary version of obiscript.
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Former-commit-id: 0d2c0fc5e33e0873ba5c04aca4cf7dd69aa83c90
2024-03-06 12:56:44 -03:00
7bd073ccd4
First version of obisplit and patch a bug in the new workers API
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Former-commit-id: f28af9f104c08d68e29fd866739d8dd58241da63
2024-03-03 11:16:24 -04:00
0f3871d203
Change the API of workers
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Former-commit-id: 9b07306edd8cf28266f86f95823948fa99d39ea9
2024-03-02 16:03:46 -04:00
37c3e16d5d
Adds the option --pairing-scale to obipairing
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Former-commit-id: c60416708467f5e818e70e08b3c512014b6212f0
2023-12-07 12:28:16 +01:00
5682247ff8
Update main.go
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Former-commit-id: f2aec0d30c0d2b31a9d00c7d4adf47421123b0fb
2023-12-01 16:42:12 +01:00
8d77cc4133
Change path of the obitools pkg
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Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
2023-11-29 12:14:37 +01:00
