Faith Okamoto

👋🏽 My CV is available. 👋🏽

• Quality of life updates

  one of those easy things to neglect

  By Faith Okamoto

  Posted on December 27, 2025

  I’ve been on holiday, so this will be a quick one. We have a release scheduled for Monday that I suspect I’m going to end up doing. That led to me looking at the changelog for this update. There is a… pattern. [Read More]

  Tags:

  • errors
  • usability

• Understanding an API

  December 2025

  By Faith Okamoto

  Posted on December 13, 2025

  It’s the holidays and I just needed to find some article to write about. So I’m going with the marker paper for minimap2. It’s a hugely important tool in my field but I don’t think I’ve ever looked at its code. [Read More]

  Tags:

  • published-code-critique
  • documentation
  • comments

• Documenting the magic button

  When simplifications become confusing

  By Faith Okamoto

  Posted on December 6, 2025

  I’ve been running someone else’s pipeline (that most terrible of tasks) and, unsurprisingly, have issues. This post will be about one of those issues. [Read More]

  Tags:

  • documentation
  • pipeline

• But why?

  November 2025

  By Faith Okamoto

  Posted on November 23, 2025

  A Google Scholar alert sent me some clickbait recently. Well, clickbait for folks who work on structural variation (SV) genotyping. A preprint claiming to genotype SVs using short reads just as well as standard long read methods. I prefer to not critique preprints, but lucky me, its repository links to... [Read More]

  Tags:

  • published-code-critique
  • comments
  • self-documenting

• How verbose is that log?

  Debugging woes

  By Faith Okamoto

  Posted on November 8, 2025

  I’ve had a run of very frustrating debugging recently. This post is inspired by one of the issues I ran into: a verbose log that left out crucial information. [Read More]

  Tags:

  • debugging
  • logs

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