Add proportional subsampling and Shannon entropy calculation

Introduces `--subsample N` and `--shannon` CLI flags to cap retained variable families via proportional reservoir sampling and compute per-family Shannon entropy. Updates the family scanning API to support explicit selection filtering with early-exit optimization, resolving an indexing drift issue in monomorphic layers. Streams entropy metrics for 15-state and 4-nucleotide spaces directly to CSV while maintaining parallel processing across sibling layers.

This commit is contained in:

Eric Coissac

2026-08-16 21:31:06 +02:00

parent f5e4bbfc6b

commit 45b19503a1

17 changed files with 841 additions and 70 deletions

.gitignore

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@@ -26,6 +26,7 @@ benchmark/specific_index_count
 benchmark/specific_index_presence
 TNT
 phyg
 biblio
 *.tnt
 *.tre
 *.phy