README.md
pyproject.toml
setup.py
extra/HMM_class.py
extra/hmm_algorithms_v2.py
extra/set_emissions_v2.py
extra/set_parameters_helper_functions_v2.py
extra/set_states_v2.py
extra/set_transitions_v2.py
orfeus/__init__.py
orfeus/orfeusbuild.py
orfeus/orfeusrun.py
orfeus.egg-info/PKG-INFO
orfeus.egg-info/SOURCES.txt
orfeus.egg-info/dependency_links.txt
orfeus.egg-info/entry_points.txt
orfeus.egg-info/requires.txt
orfeus.egg-info/top_level.txt
orfeus/coverage/__init__.py
orfeus/coverage/accuracy.py
orfeus/coverage/count.py
orfeus/coverage/sensitivity.py
orfeus/coverage/specificity.py
orfeus/coverage/threshold.py
orfeus/hmm/__init__.py
orfeus/hmm/algorithms.py
orfeus/hmm/helper.py
orfeus/hmm/run.py
orfeus/hmm/simulation.py
orfeus/output/__init__.py
orfeus/output/logo.py
orfeus/output/plots.py
orfeus/output/text.py
orfeus/parameters/__init__.py
orfeus/parameters/emissions.py
orfeus/parameters/helper.py
orfeus/parameters/set.py
orfeus/parameters/states.py
orfeus/parameters/transitions.py
orfeus/parsers/__init__.py
orfeus/parsers/bg.py
orfeus/parsers/data.py
orfeus/parsers/fa.py
orfeus/parsers/gtf.py
orfeus/parsers/wig.py
tests/debug.py