Releases · imallona/amet

[0.1.1] - 2026-05-15

--features accepts multiple BEDs, scored in one cell-read pass. Each BED
writes its own triplet <prefix>.<label>.{cell_feature,feature,pair_counts}.tsv.gz
(<label> is the BED basename). A single --features keeps the old paths.

Streamed scoring: rows written per cell, aggregates updated as it goes. Peak
memory is bounded by threads x one cell-and-feature-set batch, not the full
cells x feature-sets x features matrix.
Cells scored in parallel. cell_feature/pair_counts row order is now
cell-interleaved (key by cell_id); feature.tsv.gz stays sorted.
Workflow: CRC/Ecker/Argelaguet feature rules run amet once per cell-group
combo. Output names changed from <annotation>_<combo>.* to
<combo>.<annotation>.*.
Makefile: CORES 16 -> 40, ULIMIT_KB 200 GB -> 100 GB per process.

Pair counting rewritten: compact observed-CpG window, all lags in one sweep.
Cost scales with observed CpGs, not the feature's total CpG count.

--i-max-lag 0 is rejected by the CLI; it no longer panics (lag 1 is needed
for JSD).
features_label strips .bgz and .bed.bgz.
setup_barbara_links.sh and sync_from_barbara.sh resolved the repo root one
level too shallow, placing results/ symlinks under workflow/.