FiberHMM 2.14.0 — DddA radial nucleosome recaller

DddA radial nucleosome recaller

⚠️ Experimental — early / still in testing. The DddA radial recaller is new and under active validation. Inspect nucleosome calls before relying on them and please report issues.

DddA deaminates inside nucleosomes, so the default accessible-cut split shatters them. This release adds a DddA-specific nucleosome recall mode: a match-filter against a single-nucleosome radial deamination template (deamination rate vs distance-from-dyad) places dyads, then edges are set at the protected→linker density transition.

What's new

• fiberhmm-call --enzyme ddda now runs nucleosome recall on by default, using the bundled radial profile (ddda_nuc_profile.json) instead of the accessible-cut Kadane split.
• New core: NucProfile + load_nuc_profile, a vectorized per-read dyad LLR (np.correlate of deaminated/protected opportunity masks against the template), greedy min-separation dyad placement, and a density-transition edge finder.
• Threaded through both the streaming and region-parallel fused pipelines (profile loaded once per worker).

Compatibility

• Non-DddA behavior is unchanged — the new nuc_profile path defaults off everywhere; Hia5/DddB calling is byte-for-byte identical.
• Verified end-to-end on real DddA fiber data through both pipeline paths; full test suite green.

pip install -U fiberhmm