obitools/obitools4
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56f5fe33d726b493a6e0bcfdbe095068421db5f1
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3 Commits
Author SHA1 Message Date
Eric Coissac 56f5fe33d7 Implement strict word finding and sequence filtering 
This introduces new structures for defining sequence roles and constraints, core logic for strict word identification, and comprehensive unit tests to ensure accuracy and correct behavior.
 2026-11-03 22:34:10 +11:00
Eric Coissac 3f0ca993d2 Implement k-mer counting and sequence handling 
Introduces the SeqKmerCounter structure for parallel k-mer counting, refactors sequence reading and writing logic, and adds comprehensive test coverage for various sequence scenarios.
 2026-11-03 22:33:44 +11:00
Eric Coissac e511650f5b Refactor similarity engine and implement parallel clustering 
Introduces parallel processing for clustering, refines scoring mechanisms, and expands test coverage for the alignment functionality.

This change introduces parallel processing capabilities within the clustering logic, updates the core similarity engine with new data structures and scoring methods, and implements a comprehensive test suite for the alignment tool. It also adds new command-line options for configuring alignment parameters and reference lengths.
 2026-11-03 14:04:32 +11:00