00dcd78e84
Refactor k-mer encoding and frequency filtering with KmerSet
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This commit refactors the k-mer encoding logic to handle ambiguous bases more consistently and introduces a KmerSet type for better management of k-mer collections. The frequency filter now works with KmerSet instead of roaring bitmaps directly, and the API has been updated to support level-based frequency queries. Additionally, the commit updates the version and commit hash.
2026-02-05 14:41:59 +01:00
60f27c1dc8
Add error handling for ambiguous bases in k-mer encoding
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This commit introduces error handling for ambiguous DNA bases (N, R, Y, W, S, K, M, B, D, H, V) in k-mer encoding. It adds new functions IterNormalizedKmersWithErrors and EncodeNormalizedKmersWithErrors that track and encode the number of ambiguous bases in each k-mer using error markers in the top 2 bits. The commit also updates the version string to reflect the latest changes.
2026-02-04 21:45:08 +01:00
b49aba9c09
Implémentation du filtrage unique basé sur séquence et catégories
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Ajout d'une fonctionnalité pour le filtrage unique qui prend en compte à la fois la séquence et les catégories.
- Modification de la fonction ISequenceChunk pour accepter un classifieur unique optionnel
- Implémentation du traitement unique sur disque en utilisant un classifieur composite
- Mise à jour du classifieur utilisé pour le tri sur disque
- Correction de la gestion des clés de unicité en utilisant le code et la valeur du classifieur
- Mise à jour du numéro de commit
2026-01-14 19:18:17 +01:00
0678181023
Refactor chunk processing and update version commit
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Optimize chunk processing by moving variable declarations inside the loop and update the commit hash in version.go to reflect the latest changes.
2026-01-14 18:46:04 +01:00
ac0d3f3fe4
Update obiuniq for very large dataset
2025-12-18 14:11:11 +01:00
547135c747
End of obilowmask
2025-12-03 11:49:07 +01:00
86e60aedd0
obicsv bug with stat on value map fields
2025-11-21 14:03:31 +01:00
e65b2a5efe
obimatrix bugs
2025-11-21 13:24:06 +01:00
ccc827afd3
finalise obilowmask
2025-11-18 15:33:08 +01:00
4603d7973e
implementation de obilowmask
2025-11-18 15:30:20 +01:00
2d7dc7d09d
debug taxonomy core dump
2025-11-05 19:01:15 +01:00
0844dcc607
bug obimatrix
2025-10-28 13:57:31 +01:00
7f4ebe757e
Bug obiuniq - don't clean the chunks
2025-10-28 13:50:22 +01:00
d17a9520b9
work on obiclean chimera detection
2025-10-20 17:29:47 +02:00
29bf4ce871
add a feature to obimatrix adding obicsv option to obimatrix
2025-10-20 16:34:58 +02:00
82b6bb1ab6
correct a bug in func (worker SeqWorker) ChainWorkers(next SeqWorker) SeqWorker
2025-08-11 15:09:49 +02:00
6d204f6281
Patch the fastq detector
2025-08-08 10:23:03 -04:00
7a6d552450
Changes to be committed:
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modified: pkg/obioptions/version.go
2025-08-07 17:01:48 -04:00
730d448fc3
Allows for only one cpu and it should work
2025-08-06 16:09:25 -04:00
04f3af3e60
some renaming of functions
2025-08-06 15:54:50 -04:00
ed28d3fb5b
Adds a --u-to-t option
2025-07-07 15:35:26 +02:00
43b285587e
Debug on taxonomy extraction and CSV conversion
2025-07-07 15:29:40 +02:00
235a7e202a
Update obisummary to account new obiseq.StatsOnValues type
2025-06-19 17:21:30 +02:00
27fa984a63
Patch obimatrix accoring to the new type obiseq.StatsOnValues
2025-06-19 16:51:53 +02:00
add9d89ccc
Patch the Min and Max values of the expression language
2025-06-19 16:43:26 +02:00
9965370d85
Manage a lock on StatsOnValues
2025-06-17 16:46:11 +02:00
8a2bb1fe82
Changes to be committed:
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modified: pkg/obioptions/version.go
modified: pkg/obiseq/merge.go
2025-06-17 12:11:35 +02:00
efc3f3af29
Patch a concurrent access problem
2025-06-17 12:05:42 +02:00
1c6ab1c559
Changes to be committed:
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modified: pkg/obingslibrary/multimatch.go
modified: pkg/obioptions/version.go
2025-06-17 09:06:42 +02:00
38dcd98d4a
Patch the genbank parser automata
2025-06-17 08:52:45 +02:00
7b23985693
Add _ to allowed in taxid
2025-06-06 14:37:57 +02:00
d31e677304
Patch a bug in obitag
2025-06-04 14:47:28 +02:00
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
3424d3057f
Changes to be committed:
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modified: pkg/obiformats/ngsfilter_read.go
modified: pkg/obioptions/version.go
modified: pkg/obiutils/mimetypes.go
2025-05-14 14:53:25 +02:00
f9324dd8f4
add min and max to the obitools expression language
2025-05-13 16:03:03 +02:00
f1b9ac4a13
Update the expression language
2025-05-07 20:45:05 +02:00
e065e2963b
Update the install script
2025-05-01 11:45:46 +02:00
13ff892ac9
Patch type mismatch in apat C library
2025-04-23 16:14:10 +02:00
c0ecaf90ab
Add the --number option to obiannotate
2025-04-22 18:35:51 +02:00
a57cfda675
Make the replace function of the eval language accepting regex
2025-04-10 15:17:15 +02:00
0aec5ba4df
change the tests according to the corrections in obipairing
2025-04-04 17:10:17 +02:00
67e5b6ef24
Changes to be committed:
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modified: pkg/obioptions/version.go
2025-04-04 17:02:45 +02:00
3b1aa2869e
Changes to be committed:
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modified: pkg/obioptions/version.go
2025-04-04 17:01:20 +02:00
7542e33010
Several bugs dicoverd during the doc writing
2025-04-04 16:59:27 +02:00
03b5ce9397
Patch a bug in obitag when some reference sequences have taxid absent from the taxonomy
2025-03-27 16:45:02 +01:00
2d52322876
Patch a bug in the obi2 annotation parser on map indexed by integers
2025-03-27 14:54:13 +01:00
fd80249b85
Patch a bug in obitag when a taxon from the reference library is unknown in the taxonomy
2025-03-27 14:28:15 +01:00
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
2ab6f67d58
Add a progress bar to chimera detection
2025-03-25 08:37:27 +01:00
8b379d30da
Adds the --newick-output option to the obitaxonomy command
2025-03-14 14:24:12 +01:00
Eric Coissac