LICENSE
README.md
pyproject.toml
src/segshape/__init__.py
src/segshape/cli.py
src/segshape.egg-info/PKG-INFO
src/segshape.egg-info/SOURCES.txt
src/segshape.egg-info/dependency_links.txt
src/segshape.egg-info/entry_points.txt
src/segshape.egg-info/requires.txt
src/segshape.egg-info/top_level.txt
src/segshape/align/__init__.py
src/segshape/align/anchored.py
src/segshape/align/cli.py
src/segshape/data/__init__.py
src/segshape/data/kmer_models/build_levels_with_stdv.py
src/segshape/data/kmer_models/f5c_rna004_9mer_template_5_to_3.csv
src/segshape/data/kmer_models/ont_rna002_5mer_levels_v1_5_to_3.txt
src/segshape/data/kmer_models/ont_rna002_5mer_levels_v1_with_stdv_5_to_3.txt
src/segshape/data/kmer_models/ont_rna002_template_median69pA_3_to_5.model
src/segshape/data/kmer_models/ont_rna002_template_median69pA_5_to_3.model
src/segshape/data/kmer_models/ont_rna004_9mer_levels_v1_5_to_3.txt
src/segshape/data/kmer_models/ont_rna004_9mer_levels_v1_with_stdv_5_to_3.txt
src/segshape/data/rnafold_params/rna_andronescu2007.par
src/segshape/evaluate/__init__.py
src/segshape/evaluate/build_summary.py
src/segshape/evaluate/cli.py
src/segshape/evaluate/filter_ll.py
src/segshape/evaluate/fold_out.py
src/segshape/evaluate/fold_out_all.py
src/segshape/evaluate/pipeline.py
src/segshape/evaluate/summarize.py
src/segshape/fold/__init__.py
src/segshape/fold/cli.py
src/segshape/fold/rnafold.py
src/segshape/io/__init__.py
src/segshape/io/cli.py
src/segshape/io/dorado_mv.py
src/segshape/io/pod5_index.py
src/segshape/plot/__init__.py
src/segshape/plot/alignment_path.py
src/segshape/plot/cli.py
src/segshape/plot/dorado_mv.py
src/segshape/plot/segment_qc.py
src/segshape/reactivity/__init__.py
src/segshape/reactivity/calling.py
src/segshape/reactivity/cli.py
src/segshape/segment/__init__.py
src/segshape/segment/cli.py
src/segshape/segment/events.py
tests/test_package.py