FiberHMM 2.13.0 — Nucleosome recaller

Highlights

Per-read LLR nucleosome recaller (default on)

A new evidence-driven recaller refines the HMM's nucleosome calls on each read:

• Split over-merged footprints on accessible (m6A / deamination) evidence using a log-likelihood-ratio maximum-subarray scan — no size prior, evidence only.
• Edge refinement trims Viterbi overshoot to a conservative protected core and encodes left/right edge sharpness.
• Evidence-gated phase prior (Pass 2, opt-in via --phase-nrl) splits long footprints at periodicity-predicted linkers using a lowered threshold — a cut still requires real local evidence, so signal-deserts are never split. The nucleosome repeat length is auto-estimated (anchored near 185 bp).

nuc+QQQ / tf+QQQ molecular-annotation tags

Nucleosome and TF calls now carry per-annotation quality and edge-sharpness bytes alongside the legacy ns/nl/as/al tags (kept for FIRE/fibertools compatibility).

fibertools compatibility

• Molecular-frame coordinates: all interval tags (ns/nl/as/al and the molecular-annotation tags) are now written in molecular (original-fiber) coordinates. This corrects a frame mismatch on reverse-strand reads where annotations could be mis-placed downstream. Validated against fibertools-rs ft extract / ft fire.
• Clean, sorted, non-overlapping nucleosome + MSP tiling (required by fibertools/FIRE).
• A coord=molecular header marker and @PG provenance are recorded on output.

DAF strand-swap chimera filter

Reads mixing forward- and reverse-strand deaminations (C→T and G→A in one molecule) are detected and filtered by default, with a count reported. Disable with --keep-chimeras.

Circular-genome support

The recaller, tiling, and MSP derivation are circular-aware, correctly handling nucleosomes that wrap the molecular origin.

Install

pip install --upgrade fiberhmm