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FiberHMM v2.1.0

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@mtcicero26 mtcicero26 released this 06 Mar 15:46
· 547 commits to main since this release
v2.1.0
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What's New

Posteriors Export (fiberhmm-posteriors)

New standalone CLI for exporting per-position HMM posterior probabilities (P(footprint) per position per read).

Two output formats:

  • Gzipped TSV — no extra dependencies, base64-encoded uint8 posteriors
  • HDF5 — streaming batched writes, requires pip install h5py

Format is auto-detected from file extension (.tsv.gz → TSV, .h5/.hdf5 → HDF5), or set explicitly with --format.

# TSV (no extra deps)
fiberhmm-posteriors -i tagged.bam -m model.json -o posteriors.tsv.gz -c 4

# HDF5 (requires h5py)
fiberhmm-posteriors -i tagged.bam -m model.json -o posteriors.h5 -c 4

Other Changes

  • New optional dependency group: pip install fiberhmm[posteriors] (installs h5py)
  • pip install fiberhmm[all] now includes h5py
  • Removed auxiliary DAF-seq preprocessing examples
  • --output-posteriors flag on fiberhmm-apply now auto-activates when posteriors package is present

Install / Upgrade

pip install --upgrade fiberhmm
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