Eric Coissac
e3c41fc11b
Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup
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Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup
This commit introduces Jaccard distance and similarity methods for KmerSet and KmerSetGroup.
For KmerSet:
- Added JaccardDistance method to compute the Jaccard distance between two KmerSets
- Added JaccardSimilarity method to compute the Jaccard similarity between two KmerSets
For KmerSetGroup:
- Added JaccardDistanceMatrix method to compute a pairwise Jaccard distance matrix
- Added JaccardSimilarityMatrix method to compute a pairwise Jaccard similarity matrix
Also includes:
- New DistMatrix implementation in pkg/obidist for storing and computing distance/similarity matrices
- Updated version handling with bump-version target in Makefile
- Added tests for all new methods
2026-02-05 17:39:23 +01:00
Eric Coissac
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
Eric Coissac
937a483aa6
Changes to be committed:
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modified: Makefile
2025-03-12 12:55:41 +01:00
Eric Coissac
dada70e6b1
Changes to be committed:
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modified: Makefile
2025-03-12 12:49:34 +01:00
Eric Coissac
50d11ce374
Add a pre-push git-hook to run tests on obitools commands before pushing on master
2025-03-08 18:56:02 +01:00
Eric Coissac
52d5f6fe11
make makefile crashing on test error
2025-03-08 16:54:24 +01:00
Eric Coissac
4588bf8b5d
Patch the make file to fail on error
2025-02-19 15:55:07 +01:00
Eric Coissac
48138b605c
Changes to be committed:
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modified: .github/workflows/obitest.yml
modified: Makefile
modified: obitests/obitools/obicount/test.sh
2025-02-19 14:37:05 +01:00
Eric Coissac
443a9b3ce3
Changes to be committed:
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modified: Makefile
modified: obitests/obitools/obicount/test.sh
2025-02-19 14:28:49 +01:00
Eric Coissac
7e90537379
For run of test using bash in makefile
2025-02-19 13:58:52 +01:00
Eric Coissac
bd4a0b5ca5
Essais d'une google action pour lancer les tests des obitools
2025-02-19 13:45:43 +01:00
Eric Coissac
952f85f312
A first trial of a test for obicount
2025-02-19 13:17:36 +01:00
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
e25c3b7365
Bug in the json parsing
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Former-commit-id: e652b04b9fa7e11124eb5930c7bec4613c808758
2024-03-19 13:50:13 +01:00
38c49e9f38
Switch GOPATH to the local directory in Makefile
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Former-commit-id: ae00f1136021e6fcd5047aadb4762653cf003d5d
2024-02-27 07:22:57 +01:00
45ea4dacf7
Every small changes to include into Release 4.0.4
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Former-commit-id: b2a48c5b5c471f072785e02d4bb0f149a09cdf6f
2023-08-27 17:22:51 +02:00
98eac2360c
adds a rule to update packages and push the corresponding updates module files
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Former-commit-id: 1ffa805e74571f9d970dcb185f187dd586c1a190
2023-03-21 22:02:18 +07:00
6b52dc0700
Correct the Makefile for a default rule
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Former-commit-id: 7ac32f3f9778842fecd65cdd796b81f61b7fa41f
2023-03-02 20:48:55 +07:00
6c5fc8f65b
Save change in various files
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Former-commit-id: 428f8ee77c584b79cc2ef45eef2902c3e0754c77
2023-02-23 23:45:41 +01:00
5dbf8d6203
remove the g prefix by default
2023-02-02 13:11:04 +01:00
f14860a486
Patch header parting and formatiing
2022-05-27 11:53:29 +03:00
f18cc034bb
add an option alias -O for the old obi format
2022-02-24 07:26:55 +01:00
191570f675
First attempt of a Makefile originally copied from https://raw.githubusercontent.com/vincentbernat/hellogopher/master/Makefile
2022-01-14 15:21:00 +01:00
