feat: add metadata-driven k-mer filtering for rebuild command

Introduces a metadata-driven filtering system for the rebuild command, classifying genomes into ingroup and outgroup categories using exact, inequality, and hierarchical path predicates. Implements a GroupQuorumFilter to enforce configurable presence thresholds and fraction constraints per group. Refactors the command to replace global quorum filters with this unified approach, converts the presence flag to a threshold parameter, and adds corresponding documentation and MkDocs navigation.
2026-06-04 20:26:53 +02:00
parent edc18b4908
commit 476c7a6394
7 changed files with 470 additions and 33 deletions
@@ -49,6 +49,7 @@ nav:
      - PersistentCompactIntVec: implementation/persistent_compact_int_vec.md
      - PersistentBitVec: implementation/persistent_bit_vec.md
      - Merge command: implementation/merge.md
+      - Rebuild filters: implementation/rebuild_filter.md
  - Architecture:
      - Sequences: architecture/sequences/invariant.md
      - Kmer index: architecture/index_architecture.md