feat: add pairwise distance computation and phylogenetic trees

This commit introduces a new `distance` CLI subcommand that computes pairwise genomic distance matrices using configurable metrics (Jaccard, Hamming, Bray-Curtis, Euclidean, and Hellinger). It optionally generates phylogenetic trees (NJ or UPGMA) in Newick format and outputs results as CSV. The implementation adds a robust distance computation backend that dynamically routes to optimized backends based on index configuration, supports parallel iteration, and gracefully handles missing data. Additionally, it adds a `dump` task for exporting k-mer to genome mappings as CSV, introduces an `InvalidInput` error variant, updates dependencies to support numerical operations and tree construction, and performs minor module reorganizations.
2026-05-21 11:47:35 +02:00
parent 9e1d6f2f25
commit 3fa1dbf8cc
13 changed files with 512 additions and 7 deletions
@@ -7,6 +7,9 @@ edition = "2024"
 obikpartitionner = { path = "../obikpartitionner" }
 obiskio          = { path = "../obiskio" }
 obisys           = { path = "../obisys" }
+obicompactvec    = { path = "../obicompactvec" }
+obilayeredmap    = { path = "../obilayeredmap" }
+ndarray          = "0.16"
 rayon            = "1"
 serde            = { version = "1", features = ["derive"] }
 serde_json       = "1"