On the fast5_research dependency¶

The original fast5_research module hasn't been updated in 3 years, and has old dependencies. Instead of opting to vendorize the fast5_research code, we created a fork and updated it. This allows us to read/write .fast5 files used in our ONT measurements. Note that the most important part of the API for this is fast5_research.BulkFast5.

fast5_research is bundled in poreflow, so does not need to be installed seperately.

Process¶

Thankfully, a lot of the fast5_research was tested. This meant we could quickly clean up and fix the source code using an LLM (in this case Gemini CLI). Gemini was not able to fix all bugs, so some manual research into the module was needed to fix it completely. Once the source code was fixed, the tests were reformatted for clarity.

Changes to the module¶

• Bugfixes
• Dependency updates
• progressbar dependency was replaced by tqdm
• Tests were rewritten to use the cleaner pytest rather than unittest