LICENSE
README.md
apply_model.py
extract_tags.py
fiberhmm_utils.py
generate_probs.py
pyproject.toml
train_model.py
fiberhmm/__init__.py
fiberhmm.egg-info/PKG-INFO
fiberhmm.egg-info/SOURCES.txt
fiberhmm.egg-info/dependency_links.txt
fiberhmm.egg-info/entry_points.txt
fiberhmm.egg-info/requires.txt
fiberhmm.egg-info/top_level.txt
fiberhmm/cli/__init__.py
fiberhmm/cli/apply.py
fiberhmm/cli/common.py
fiberhmm/cli/extract_tags.py
fiberhmm/cli/generate_probs.py
fiberhmm/cli/train.py
fiberhmm/cli/utils.py
fiberhmm/core/__init__.py
fiberhmm/core/bam_reader.py
fiberhmm/core/hmm.py
fiberhmm/core/model_io.py
fiberhmm/inference/__init__.py
fiberhmm/inference/bam_output.py
fiberhmm/inference/engine.py
fiberhmm/inference/parallel.py
fiberhmm/inference/stats.py
fiberhmm/probabilities/__init__.py
fiberhmm/probabilities/context_counter.py
fiberhmm/probabilities/stats.py
fiberhmm/probabilities/utils.py
tests/test_bam_reader.py
tests/test_cli_common.py
tests/test_hmm.py
tests/test_inference_engine.py
tests/test_inference_parallel.py
tests/test_model_io.py
tests/test_package_consistency.py