FiberHMM 2.13.2 — fiberhmm-recall-nucs: nucleosome recall without re-running the HMM

New: fiberhmm-recall-nucs

A second-pass nucleosome recaller that runs on an fiberhmm-apply-tagged BAM without re-running the HMM — analogous to how fiberhmm-recall-tfs works. It reuses the existing ns/nl/as/al segmentation: re-derives nucleosome boundaries, re-computes MSPs, and recalls TFs in one pass, so you can iterate on recall parameters cheaply.

• Equivalent to the recall stage of the full call pipeline, skipping the expensive apply/Viterbi step.
• fiberhmm-recall-tfs --recall-nucs runs the same nucleosome→MSP→TF recall path.
• Linear reads (a tags-reconstructed result carries no per-read circular tiling).

pip install -U fiberhmm