├── .gitignore ├── .travis.yml ├── CHANGELOG.md ├── LICENSE.md ├── MANIFEST.in ├── Makefile ├── README.md ├── dev_requirements.txt ├── docs ├── cmdline.rst ├── conf.py ├── examples.rst └── index.rst ├── fast5_research ├── __init__.py ├── extract.py ├── fast5.py ├── fast5_bulk.py ├── test │ ├── data │ │ ├── abf2bulkfast5.fast5 │ │ ├── additional_test_file.fast5 │ │ ├── elec3_example.fast5 │ │ ├── example_basecall_squiggle_mapping.fast5 │ │ ├── example_template.bc_path │ │ ├── example_template.bc_scale │ │ ├── example_template.events │ │ ├── example_template.map_path │ │ ├── example_template.map_post │ │ ├── example_template.map_scale │ │ ├── example_template.model │ │ └── recursive │ │ │ ├── 1 │ │ │ └── fake.fast5 │ │ │ ├── 2 │ │ │ └── fake.fast5 │ │ │ ├── fake1.fast5 │ │ │ ├── fake2.fast5 │ │ │ └── fake3.fast5 │ ├── test_fast5.py │ ├── test_fast5_basecalling_and_mapping.py │ ├── test_fast5_bulk.py │ └── test_iterate.py └── util.py ├── requirements.txt └── setup.py /.gitignore: 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