500144051a
Add jj Makefile targets and k-mer encoding utilities
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Add new Makefile targets for jj operations (jjnew, jjpush, jjfetch) to streamline commit workflow.
Introduce k-mer encoding utilities in pkg/obikmer:
- EncodeKmers: converts DNA sequences to encoded k-mers
- ReverseComplement: computes reverse complement of k-mers
- NormalizeKmer: returns canonical form of k-mers
- EncodeNormalizedKmers: encodes sequences with normalized k-mers
Add comprehensive tests for k-mer encoding functions including edge cases, buffer reuse, and performance benchmarks.
Document k-mer index design for large genomes, covering:
- Use cases and objectives
- Volume estimations
- Distance metrics (Jaccard, Sørensen-Dice, Bray-Curtis)
- Indexing options (Bloom filters, sorted sets, MPHF)
- Optimization techniques (k-2-mer indexing)
- MinHash for distance acceleration
- Recommended architecture for presence/absence and counting queries
2026-02-04 14:27:10 +01:00
740f66b4c7
Merge pull request #71 from metabarcoding/push-onwzsyuooozn
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Implémentation du filtrage unique basé sur séquence et catégories
2026-01-14 19:19:27 +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
52244cdb64
Merge pull request #70 from metabarcoding/push-kuwnszsxmxpn
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Refactor chunk processing and update version commit
2026-01-14 18:47:17 +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
f55dd553c7
Merge pull request #68 from metabarcoding/push-rrulynolpprl
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Push rrulynolpprl
2026-01-14 17:44:36 +01:00
4a383ac6c9
Merge branch 'master' into push-rrulynolpprl
2025-12-18 14:12:56 +01:00
371e702423
obiannotate --cut bug
2025-12-18 14:11:11 +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
f4a919732e
Merge pull request #65 from metabarcoding/push-yurwulsmpxkq
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End of obilowmask
2025-11-26 12:13:08 +01:00
e681666aaa
End of obilowmask
2025-11-26 11:14:56 +01:00
adf2486295
Merge pull request #64 from metabarcoding/push-yurwulsmpxkq
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End of obilowmask
2025-11-24 15:36:20 +01:00
272f5c9c35
End of obilowmask
2025-11-24 15:27:38 +01:00
c1b9503ca6
Merge pull request #63 from metabarcoding/push-vypwrurrsxuk
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obicsv bug with stat on value map fields
2025-11-21 14:04:34 +01:00
86e60aedd0
obicsv bug with stat on value map fields
2025-11-21 14:03:31 +01:00
961abcea7b
Merge pull request #61 from metabarcoding/push-mvxssvnysyxn
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Push mvxssvnysyxn
2025-11-21 13:25:19 +01:00
57c65f9d50
obimatrix bug
2025-11-21 13:24:24 +01:00
e65b2a5efe
obimatrix bugs
2025-11-21 13:24:06 +01:00
3e5f3f76b0
Merge pull request #60 from metabarcoding/push-qpnzxskwpoxo
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Push qpnzxskwpoxo
2025-11-18 15:35:41 +01:00
ccc827afd3
finalise obilowmask
2025-11-18 15:33:08 +01:00
cef29005a5
debug url reading
2025-11-18 15:30:20 +01:00
4603d7973e
implementation de obilowmask
2025-11-18 15:30:20 +01:00
8bc47c13d3
Merge pull request #58 from metabarcoding/push-vxkqkkrokwuz
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debug obimultiplex
2025-11-06 15:44:31 +01:00
07cdd6f758
debug obimultiplex
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bug option obimultiplex
2025-11-06 15:43:13 +01:00
432da366e2
Merge pull request #57 from metabarcoding/push-ywktmvpvtvmv
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debug taxonomy core dump
2025-11-05 19:07:41 +01:00
2d7dc7d09d
debug taxonomy core dump
2025-11-05 19:01:15 +01:00
5e12ed5400
Merge pull request #56 from metabarcoding/push-tnrvpwvqtzyo
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update install script
2025-11-04 18:11:21 +01:00
7500ee1d15
update install script
2025-11-04 18:09:15 +01:00
5a1d66bf06
Merge pull request #53 from metabarcoding/push-skmxzrzulvtq
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Push skmxzrzulvtq
2025-10-28 14:27:19 +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
5150947e23
Merge pull request #51 from metabarcoding/push-urtwmwktsrru
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Push urtwmwktsrru
2025-10-20 17:41:33 +02:00
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
d7ed9d343e
Update install_obitools.sh for missing directory
2025-10-15 08:32:06 +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
412b54822c
Patch a bug in obliclean for d>1 leading to some instability in the result
2025-08-07 17:01:38 -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
997b6e8c01
correct the fastq detector for distinguish with a csv ngsfilter
2025-08-06 15:52:54 -04:00
f239e8da92
Rename ISequenceChunk
2025-08-05 08:49:45 -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
8d53d253d4
Add a reading option on readers to convet U to T
2025-07-07 15:29:07 +02:00
8c26fc9884
Add a new test on obisummary
2025-07-07 15:28:29 +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
Eric Coissac