fiberhmm 2.0.0__tar.gz

fiberhmm-2.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024-2026 FiberHMM Authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

fiberhmm-2.0.0/PKG-INFO

@@ -0,0 +1,328 @@
+Metadata-Version: 2.4
+Name: fiberhmm
+Version: 2.0.0
+Summary: Hidden Markov Model for calling chromatin footprints from fiber-seq and DAF-seq data
+Author: FiberHMM Authors
+License: MIT
+Project-URL: Homepage, https://github.com/fiberseq/FiberHMM
+Project-URL: Documentation, https://github.com/fiberseq/FiberHMM#readme
+Project-URL: Repository, https://github.com/fiberseq/FiberHMM
+Project-URL: Issues, https://github.com/fiberseq/FiberHMM/issues
+Keywords: bioinformatics,chromatin,fiber-seq,DAF-seq,hidden-markov-model,nucleosome,footprinting,epigenetics,single-molecule
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.7
+Requires-Dist: pandas>=1.3
+Requires-Dist: pysam>=0.19
+Requires-Dist: tqdm>=4.60
+Provides-Extra: numba
+Requires-Dist: numba>=0.55; extra == "numba"
+Provides-Extra: plots
+Requires-Dist: matplotlib>=3.5; extra == "plots"
+Provides-Extra: all
+Requires-Dist: numba>=0.55; extra == "all"
+Requires-Dist: matplotlib>=3.5; extra == "all"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: black>=23.0; extra == "dev"
+Requires-Dist: ruff>=0.1; extra == "dev"
+Dynamic: license-file
+
+# FiberHMM
+
+Hidden Markov Model toolkit for calling chromatin footprints from fiber-seq and DAF-seq single-molecule data.
+
+FiberHMM identifies nucleosome-protected regions (footprints) and accessible regions (methylase-sensitive patches, MSPs) from single-molecule DNA modification data, including m6A methylation (fiber-seq) and deamination marks (DAF-seq).
+
+## Key Features
+
+- **No genome context files** -- hexamer context computed directly from read sequences
+- **Fibertools-compatible output** -- tagged BAM with `ns`/`nl`/`as`/`al` tags, ready for downstream tools
+- **Native HMM implementation** -- no hmmlearn dependency; Numba JIT optional for ~10x speedup
+- **Region-parallel processing** -- scales linearly with cores for large genomes
+- **Multi-platform** -- supports PacBio fiber-seq, Nanopore fiber-seq, and DAF-seq
+- **Legacy model support** -- loads old hmmlearn-trained pickle/NPZ models seamlessly
+
+## Installation
+
+### Using pip
+
+```bash
+pip install fiberhmm
+```
+
+### From source
+
+```bash
+git clone https://github.com/fiberseq/FiberHMM.git
+cd FiberHMM
+pip install -e .
+```
+
+### Optional dependencies
+
+```bash
+pip install numba        # ~10x faster HMM computation
+pip install matplotlib   # --stats visualization
+```
+
+For bigBed output, install [`bedToBigBed`](https://hgdownload.soe.ucsc.edu/admin/exe/) from UCSC tools.
+
+## Quick Start
+
+### 1. Generate emission probabilities
+
+Requires accessible (naked DNA) and inaccessible (native chromatin) control BAMs:
+
+```bash
+python generate_probs.py \
+    -a accessible_control.bam \
+    -u inaccessible_control.bam \
+    -o probs/ \
+    --stats
+```
+
+### 2. Train HMM
+
+```bash
+python train_model.py \
+    -i sample.bam \
+    -p probs/tables/accessible_A_k3.tsv probs/tables/inaccessible_A_k3.tsv \
+    -o models/ \
+    --stats
+```
+
+### 3. Call footprints
+
+```bash
+python apply_model.py \
+    -i experiment.bam \
+    -m models/best-model.json \
+    -o output/ \
+    -c 8 \
+    --scores
+```
+
+### 4. Extract to BED12/bigBed
+
+```bash
+python extract_tags.py -i output/experiment_footprints.bam
+```
+
+## Pre-trained Models
+
+FiberHMM ships with pre-trained models in `models/` ready for immediate use:
+
+| Model | File | Enzyme | Platform | Mode |
+|-------|------|--------|----------|------|
+| **Hia5 PacBio** | `hia5_pacbio.json` | Hia5 (m6A) | PacBio | `pacbio-fiber` |
+| **Hia5 Nanopore** | `hia5_nanopore.json` | Hia5 (m6A) | Nanopore | `nanopore-fiber` |
+| **DddA PacBio** | `ddda_pacbio.json` | DddA (deamination) | PacBio | `daf` |
+| **DddB Nanopore** | `dddb_nanopore.json` | DddB (deamination) | Nanopore | `daf` |
+
+```bash
+# Example: call footprints with a pre-trained model
+python apply_model.py -i experiment.bam -m models/hia5_pacbio.json -o output/ -c 8
+```
+
+## Analysis Modes
+
+| Mode | Flag | Description | Target bases |
+|------|------|-------------|--------------|
+| **PacBio fiber-seq** | `--mode pacbio-fiber` | Default. m6A at A and T (both strands) | A, T (with RC) |
+| **Nanopore fiber-seq** | `--mode nanopore-fiber` | m6A at A only (single strand) | A only |
+| **DAF-seq** | `--mode daf` | Deamination at C/G (strand-specific) | C or G |
+
+All scripts accept `--mode`; context size `-k` (3-10) determines the hexamer table size.
+
+**Note on mode selection:** The `pacbio-fiber` vs `nanopore-fiber` distinction only matters for Hia5 (m6A), where PacBio detects modifications on both strands while Nanopore detects only one. For deaminase-based methods (DddA, DddB), `--mode daf` is always used regardless of sequencing platform -- the chemistry is inherently strand-specific. Accuracy may differ between platforms, but the mode is the same.
+
+## Output
+
+### BAM Tags
+
+`apply_model.py` adds footprint tags compatible with the fibertools ecosystem:
+
+| Tag | Type | Description |
+|-----|------|-------------|
+| `ns` | B,I | Nucleosome/footprint starts (0-based query coords) |
+| `nl` | B,I | Nucleosome/footprint lengths |
+| `as` | B,I | Accessible/MSP starts |
+| `al` | B,I | Accessible/MSP lengths |
+| `nq` | B,C | Footprint quality scores (0-255, with `--scores`) |
+| `aq` | B,C | MSP quality scores (0-255, with `--scores`) |
+
+### BED12/bigBed Extraction
+
+Use `extract_tags.py` to extract features from tagged BAMs for browser visualization:
+
+```bash
+# Extract all feature types to bigBed
+python extract_tags.py -i output/sample_footprints.bam
+
+# Extract only footprints
+python extract_tags.py -i output/sample_footprints.bam --footprint
+
+# Keep BED files alongside bigBed
+python extract_tags.py -i output/sample_footprints.bam --keep-bed
+```
+
+## Scripts Reference
+
+### generate_probs.py / `fiberhmm-probs`
+
+Generate emission probability tables from accessible and inaccessible control BAMs.
+
+```bash
+python generate_probs.py \
+    -a accessible_control.bam \
+    -u inaccessible_control.bam \
+    -o probs/ \
+    --mode pacbio-fiber \
+    -k 3 4 5 6 \
+    --stats
+```
+
+### train_model.py / `fiberhmm-train`
+
+Train the HMM on BAM data using precomputed emission probabilities.
+
+```bash
+python train_model.py \
+    -i sample.bam \
+    -p probs/tables/accessible_A_k3.tsv probs/tables/inaccessible_A_k3.tsv \
+    -o models/ \
+    -k 3 \
+    --stats
+```
+
+Output:
+```
+models/
+├── best-model.json      # Primary format (recommended)
+├── best-model.npz       # NumPy format
+├── all_models.json      # All training iterations
+├── training-reads.tsv   # Read IDs used for training
+├── config.json          # Training parameters
+└── plots/               # (with --stats)
+```
+
+### apply_model.py / `fiberhmm-apply`
+
+Apply a trained model to call footprints. Supports region-parallel processing.
+
+```bash
+python apply_model.py \
+    -i experiment.bam \
+    -m models/best-model.json \
+    -o output/ \
+    -c 8 \
+    --scores
+```
+
+Key options:
+
+| Flag | Default | Description |
+|------|---------|-------------|
+| `-c/--cores` | 1 | CPU cores (0 = auto-detect) |
+| `--region-size` | 10000000 | Region size for parallel chunks |
+| `--skip-scaffolds` | false | Skip scaffold/contig chromosomes |
+| `--chroms` | all | Process only these chromosomes |
+| `--scores` | false | Compute per-footprint confidence scores |
+| `-q/--min-mapq` | 20 | Min mapping quality |
+| `-e/--edge-trim` | 10 | Edge masking (bp) |
+
+### extract_tags.py / `fiberhmm-extract`
+
+Extract footprint/MSP/m6A/m5C features from tagged BAMs to BED12/bigBed.
+
+```bash
+python extract_tags.py -i output/sample_footprints.bam -o output/ -c 8
+```
+
+### fiberhmm-utils
+
+Consolidated utility for model and probability management. Four subcommands:
+
+**convert** -- Convert legacy pickle/NPZ models to JSON:
+```bash
+fiberhmm-utils convert old_model.pickle new_model.json
+```
+
+**inspect** -- Print model metadata, parameters, and emission statistics:
+```bash
+fiberhmm-utils inspect model.json
+fiberhmm-utils inspect model.json --full   # full emission table
+```
+
+**transfer** -- Transfer emission probabilities between modalities (e.g., fiber-seq to DAF-seq) using accessibility priors from a matched cell type:
+```bash
+fiberhmm-utils transfer \
+    --target daf_sample.bam \
+    --reference-bam fiberseq_footprints.bam \
+    -o daf_probs/ \
+    --mode daf \
+    --stats
+```
+
+**adjust** -- Scale emission probabilities in a model (clamped to [0, 1]):
+```bash
+fiberhmm-utils adjust model.json --state accessible --scale 1.1 -o adjusted.json
+```
+
+## Fibertools Integration
+
+FiberHMM produces BAM output with the same tag conventions used by [fibertools](https://github.com/fiberseq/fibertools-rs):
+
+- `ns`/`nl` for nucleosome footprints
+- `as`/`al` for methylase-sensitive patches (MSPs)
+- `nq`/`aq` for quality scores
+
+This means FiberHMM output can be used directly with any tool in the fibertools ecosystem, including `ft extract`, downstream analysis pipelines, and genome browsers that support fibertools-style BAM tags.
+
+## FiberBrowser
+
+FiberBrowser, a dedicated genome browser for single-molecule chromatin data, is coming soon.
+
+## Performance Tips
+
+1. **Use multiple cores**: `-c 8` (or more) for parallel processing
+2. **Adjust region size for small genomes**:
+   - Yeast (~12 MB): `--region-size 500000`
+   - Drosophila (~140 MB): `--region-size 2000000`
+   - Human/mammalian: default 10 MB is fine
+3. **Skip scaffolds**: `--skip-scaffolds` to avoid thousands of small contigs
+4. **Install numba**: `pip install numba` for ~10x faster HMM training
+
+## Model Formats
+
+| Format | Extension | Description |
+|--------|-----------|-------------|
+| **JSON** | `.json` | Primary format -- portable, human-readable |
+| NPZ | `.npz` | NumPy archive -- supported for loading |
+| Pickle | `.pickle` | Legacy format -- supported for loading |
+
+New models are always saved in JSON. Convert legacy models with:
+
+```bash
+fiberhmm-utils convert old_model.pickle new_model.json
+```
+
+## License
+
+MIT License. See [LICENSE](LICENSE) for details.

fiberhmm-2.0.0/README.md

@@ -0,0 +1,283 @@
+# FiberHMM
+
+Hidden Markov Model toolkit for calling chromatin footprints from fiber-seq and DAF-seq single-molecule data.
+
+FiberHMM identifies nucleosome-protected regions (footprints) and accessible regions (methylase-sensitive patches, MSPs) from single-molecule DNA modification data, including m6A methylation (fiber-seq) and deamination marks (DAF-seq).
+
+## Key Features
+
+- **No genome context files** -- hexamer context computed directly from read sequences
+- **Fibertools-compatible output** -- tagged BAM with `ns`/`nl`/`as`/`al` tags, ready for downstream tools
+- **Native HMM implementation** -- no hmmlearn dependency; Numba JIT optional for ~10x speedup
+- **Region-parallel processing** -- scales linearly with cores for large genomes
+- **Multi-platform** -- supports PacBio fiber-seq, Nanopore fiber-seq, and DAF-seq
+- **Legacy model support** -- loads old hmmlearn-trained pickle/NPZ models seamlessly
+
+## Installation
+
+### Using pip
+
+```bash
+pip install fiberhmm
+```
+
+### From source
+
+```bash
+git clone https://github.com/fiberseq/FiberHMM.git
+cd FiberHMM
+pip install -e .
+```
+
+### Optional dependencies
+
+```bash
+pip install numba        # ~10x faster HMM computation
+pip install matplotlib   # --stats visualization
+```
+
+For bigBed output, install [`bedToBigBed`](https://hgdownload.soe.ucsc.edu/admin/exe/) from UCSC tools.
+
+## Quick Start
+
+### 1. Generate emission probabilities
+
+Requires accessible (naked DNA) and inaccessible (native chromatin) control BAMs:
+
+```bash
+python generate_probs.py \
+    -a accessible_control.bam \
+    -u inaccessible_control.bam \
+    -o probs/ \
+    --stats
+```
+
+### 2. Train HMM
+
+```bash
+python train_model.py \
+    -i sample.bam \
+    -p probs/tables/accessible_A_k3.tsv probs/tables/inaccessible_A_k3.tsv \
+    -o models/ \
+    --stats
+```
+
+### 3. Call footprints
+
+```bash
+python apply_model.py \
+    -i experiment.bam \
+    -m models/best-model.json \
+    -o output/ \
+    -c 8 \
+    --scores
+```
+
+### 4. Extract to BED12/bigBed
+
+```bash
+python extract_tags.py -i output/experiment_footprints.bam
+```
+
+## Pre-trained Models
+
+FiberHMM ships with pre-trained models in `models/` ready for immediate use:
+
+| Model | File | Enzyme | Platform | Mode |
+|-------|------|--------|----------|------|
+| **Hia5 PacBio** | `hia5_pacbio.json` | Hia5 (m6A) | PacBio | `pacbio-fiber` |
+| **Hia5 Nanopore** | `hia5_nanopore.json` | Hia5 (m6A) | Nanopore | `nanopore-fiber` |
+| **DddA PacBio** | `ddda_pacbio.json` | DddA (deamination) | PacBio | `daf` |
+| **DddB Nanopore** | `dddb_nanopore.json` | DddB (deamination) | Nanopore | `daf` |
+
+```bash
+# Example: call footprints with a pre-trained model
+python apply_model.py -i experiment.bam -m models/hia5_pacbio.json -o output/ -c 8
+```
+
+## Analysis Modes
+
+| Mode | Flag | Description | Target bases |
+|------|------|-------------|--------------|
+| **PacBio fiber-seq** | `--mode pacbio-fiber` | Default. m6A at A and T (both strands) | A, T (with RC) |
+| **Nanopore fiber-seq** | `--mode nanopore-fiber` | m6A at A only (single strand) | A only |
+| **DAF-seq** | `--mode daf` | Deamination at C/G (strand-specific) | C or G |
+
+All scripts accept `--mode`; context size `-k` (3-10) determines the hexamer table size.
+
+**Note on mode selection:** The `pacbio-fiber` vs `nanopore-fiber` distinction only matters for Hia5 (m6A), where PacBio detects modifications on both strands while Nanopore detects only one. For deaminase-based methods (DddA, DddB), `--mode daf` is always used regardless of sequencing platform -- the chemistry is inherently strand-specific. Accuracy may differ between platforms, but the mode is the same.
+
+## Output
+
+### BAM Tags
+
+`apply_model.py` adds footprint tags compatible with the fibertools ecosystem:
+
+| Tag | Type | Description |
+|-----|------|-------------|
+| `ns` | B,I | Nucleosome/footprint starts (0-based query coords) |
+| `nl` | B,I | Nucleosome/footprint lengths |
+| `as` | B,I | Accessible/MSP starts |
+| `al` | B,I | Accessible/MSP lengths |
+| `nq` | B,C | Footprint quality scores (0-255, with `--scores`) |
+| `aq` | B,C | MSP quality scores (0-255, with `--scores`) |
+
+### BED12/bigBed Extraction
+
+Use `extract_tags.py` to extract features from tagged BAMs for browser visualization:
+
+```bash
+# Extract all feature types to bigBed
+python extract_tags.py -i output/sample_footprints.bam
+
+# Extract only footprints
+python extract_tags.py -i output/sample_footprints.bam --footprint
+
+# Keep BED files alongside bigBed
+python extract_tags.py -i output/sample_footprints.bam --keep-bed
+```
+
+## Scripts Reference
+
+### generate_probs.py / `fiberhmm-probs`
+
+Generate emission probability tables from accessible and inaccessible control BAMs.
+
+```bash
+python generate_probs.py \
+    -a accessible_control.bam \
+    -u inaccessible_control.bam \
+    -o probs/ \
+    --mode pacbio-fiber \
+    -k 3 4 5 6 \
+    --stats
+```
+
+### train_model.py / `fiberhmm-train`
+
+Train the HMM on BAM data using precomputed emission probabilities.
+
+```bash
+python train_model.py \
+    -i sample.bam \
+    -p probs/tables/accessible_A_k3.tsv probs/tables/inaccessible_A_k3.tsv \
+    -o models/ \
+    -k 3 \
+    --stats
+```
+
+Output:
+```
+models/
+├── best-model.json      # Primary format (recommended)
+├── best-model.npz       # NumPy format
+├── all_models.json      # All training iterations
+├── training-reads.tsv   # Read IDs used for training
+├── config.json          # Training parameters
+└── plots/               # (with --stats)
+```
+
+### apply_model.py / `fiberhmm-apply`
+
+Apply a trained model to call footprints. Supports region-parallel processing.
+
+```bash
+python apply_model.py \
+    -i experiment.bam \
+    -m models/best-model.json \
+    -o output/ \
+    -c 8 \
+    --scores
+```
+
+Key options:
+
+| Flag | Default | Description |
+|------|---------|-------------|
+| `-c/--cores` | 1 | CPU cores (0 = auto-detect) |
+| `--region-size` | 10000000 | Region size for parallel chunks |
+| `--skip-scaffolds` | false | Skip scaffold/contig chromosomes |
+| `--chroms` | all | Process only these chromosomes |
+| `--scores` | false | Compute per-footprint confidence scores |
+| `-q/--min-mapq` | 20 | Min mapping quality |
+| `-e/--edge-trim` | 10 | Edge masking (bp) |
+
+### extract_tags.py / `fiberhmm-extract`
+
+Extract footprint/MSP/m6A/m5C features from tagged BAMs to BED12/bigBed.
+
+```bash
+python extract_tags.py -i output/sample_footprints.bam -o output/ -c 8
+```
+
+### fiberhmm-utils
+
+Consolidated utility for model and probability management. Four subcommands:
+
+**convert** -- Convert legacy pickle/NPZ models to JSON:
+```bash
+fiberhmm-utils convert old_model.pickle new_model.json
+```
+
+**inspect** -- Print model metadata, parameters, and emission statistics:
+```bash
+fiberhmm-utils inspect model.json
+fiberhmm-utils inspect model.json --full   # full emission table
+```
+
+**transfer** -- Transfer emission probabilities between modalities (e.g., fiber-seq to DAF-seq) using accessibility priors from a matched cell type:
+```bash
+fiberhmm-utils transfer \
+    --target daf_sample.bam \
+    --reference-bam fiberseq_footprints.bam \
+    -o daf_probs/ \
+    --mode daf \
+    --stats
+```
+
+**adjust** -- Scale emission probabilities in a model (clamped to [0, 1]):
+```bash
+fiberhmm-utils adjust model.json --state accessible --scale 1.1 -o adjusted.json
+```
+
+## Fibertools Integration
+
+FiberHMM produces BAM output with the same tag conventions used by [fibertools](https://github.com/fiberseq/fibertools-rs):
+
+- `ns`/`nl` for nucleosome footprints
+- `as`/`al` for methylase-sensitive patches (MSPs)
+- `nq`/`aq` for quality scores
+
+This means FiberHMM output can be used directly with any tool in the fibertools ecosystem, including `ft extract`, downstream analysis pipelines, and genome browsers that support fibertools-style BAM tags.
+
+## FiberBrowser
+
+FiberBrowser, a dedicated genome browser for single-molecule chromatin data, is coming soon.
+
+## Performance Tips
+
+1. **Use multiple cores**: `-c 8` (or more) for parallel processing
+2. **Adjust region size for small genomes**:
+   - Yeast (~12 MB): `--region-size 500000`
+   - Drosophila (~140 MB): `--region-size 2000000`
+   - Human/mammalian: default 10 MB is fine
+3. **Skip scaffolds**: `--skip-scaffolds` to avoid thousands of small contigs
+4. **Install numba**: `pip install numba` for ~10x faster HMM training
+
+## Model Formats
+
+| Format | Extension | Description |
+|--------|-----------|-------------|
+| **JSON** | `.json` | Primary format -- portable, human-readable |
+| NPZ | `.npz` | NumPy archive -- supported for loading |
+| Pickle | `.pickle` | Legacy format -- supported for loading |
+
+New models are always saved in JSON. Convert legacy models with:
+
+```bash
+fiberhmm-utils convert old_model.pickle new_model.json
+```
+
+## License
+
+MIT License. See [LICENSE](LICENSE) for details.

fiberhmm-2.0.0/apply_model.py

@@ -0,0 +1,6 @@
+#!/usr/bin/env python3
+"""Backward-compatible wrapper. See fiberhmm/cli/apply.py"""
+from fiberhmm.cli.apply import main
+
+if __name__ == '__main__':
+    main()

fiberhmm-2.0.0/extract_tags.py

@@ -0,0 +1,6 @@
+#!/usr/bin/env python3
+"""Backward-compatible wrapper. See fiberhmm/cli/extract_tags.py"""
+from fiberhmm.cli.extract_tags import main
+
+if __name__ == '__main__':
+    main()

fiberhmm-2.0.0/fiberhmm/__init__.py

@@ -0,0 +1,10 @@
+"""
+FiberHMM - Hidden Markov Model toolkit for chromatin footprint calling
+from fiber-seq and DAF-seq single-molecule data.
+"""
+
+__version__ = "2.0.0"
+
+from fiberhmm.core.hmm import FiberHMM
+from fiberhmm.core.bam_reader import ContextEncoder, FiberRead, read_bam
+from fiberhmm.core.model_io import load_model, save_model, load_model_with_metadata

fiberhmm-2.0.0/fiberhmm/cli/__init__.py

@@ -0,0 +1,2 @@
+"""Command-line interface entry points."""
+# CLI modules are populated as scripts are moved into the package