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Eric Coissac a0d8187fd6 Implement k-mer distance metrics and constrained generation 
Adds support for Hamming distance, constrained k-mer generation, and optimized Longest Common Subsequence (LCS) calculations using scalar, batch, and SIMD methods.

This includes new methods for k-mer distance calculation, structures for k-mer constraints, and SIMD-based batch processing for LCS to improve performance and correctness.
2026-11-03 09:23:37 +11:00
..
obialign
fix: validate inputs and fix coordinate offsets in pattern matching
2026-08-19 17:25:44 +02:00
obiapat
fix: validate inputs and fix coordinate offsets in pattern matching
2026-08-19 17:25:44 +02:00
obichunk
Fix classifier cloning and reset in chunk processing
2026-02-08 15:52:25 +01:00
obicorazick
Add progress bar configuration and conditional display
2026-02-08 16:14:02 +01:00
obidefault
refactor: replace single batch size with min/max bounds and memory limits
2026-03-13 15:07:35 +01:00
obidist
Add Jaccard distance and similarity computations for KmerSet and KmerSetGroup
2026-02-05 17:39:23 +01:00
obiformats
refactor: improve FASTQ error messages with explicit filenames
2026-08-19 16:47:36 +02:00
obifp
fix: update uint128 test expectations and improve log formatting
2026-08-19 17:33:57 +02:00
obigraph
Add obiminion first version
2024-05-14 08:16:12 +02:00
obiiter
Refactor batch iterator filtering and update project configuration
2026-11-03 09:22:46 +11:00
obiitercsv
break the import cyccle
2025-01-27 17:23:07 +01:00
obikmer
Implement k-mer distance metrics and constrained generation
2026-11-03 09:23:37 +11:00
obilog
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
obilua
chore: bump version to 4.4.39
2026-04-14 14:48:29 +02:00
obingslibrary
fix: respect config defaults when --allowed-mismatches is unset
2026-08-19 16:40:48 +02:00
obioptions
Release 4.5.0
2026-08-19 17:35:06 +02:00
obiphylo
Changes to be committed:
2025-06-04 09:48:10 +02:00
obiseq
fix: correct duplicated typos in GVal function names
2026-06-02 15:00:48 +02:00
obistats
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
obisuffix
Swich to the system min and max functions and remove the version from obiutils
2024-05-30 08:27:24 +02:00
obitable
many changes ;-)
2023-12-05 15:28:29 +01:00
obitax
feat(obiconvert): add --raw-taxid option and refactor taxID formatting
2026-04-30 16:57:38 +02:00
obitools
Implement k-mer distance metrics and constrained generation
2026-11-03 09:23:37 +11:00
obiutils
feat: add JSON input support for biological sequences
2026-07-03 10:16:55 +02:00