Faith Okamoto

👋🏽 My CV is available. 👋🏽

• Provide context for code

  June 2025

  By Faith Okamoto

  Posted on June 19, 2025

  I have today off so I figured I’d do a blog post. Thought I could trust Nature to have some nice code for me to look at. Given the quality of the code for the first paper I clicked on, perhaps I’d do better to focus on computational journals in... [Read More]

  Tags:

  • published-code-critique
  • readme
  • documentation

• Using simple structs

  Name all the things!

  By Faith Okamoto

  Posted on June 7, 2025

  The last assignment for my class on plotting required sophisticated data processing and storage. My storage method of choice was a simple struct. [Read More]

  Tags:

  • naming

• Double-check your comments

  May 2025

  By Faith Okamoto

  Posted on May 24, 2025

  I usually critique biology/bioinformatics papers (since that’s my field). This month, we’re looking at a paper where I do not understand any of the jargon. [Read More]

  Tags:

  • published-code-critique
  • comments
  • last-pass

• Parameters implying other parameters

  But what does that mean?

  By Faith Okamoto

  Posted on May 17, 2025

  Some options are meant to be used together. This might be bidirectional (e.g. both a sample name and a data file) or it might be one-way (e.g. an alignment file needs a genome file, but not the other way around). In either case, using a specific optional argument requires the... [Read More]

  Tags:

  • parameters
  • errors

• Documenting options

  What choices do I have?

  By Faith Okamoto

  Posted on May 3, 2025

  I recently identified a problem with vg filter’s --tsv-out option. Namely, that a command to write “a tsv of the given fields” didn’t document which fields were possible. This command is quite important to running QC on our GAM and GAMP alignment files. Those files aren’t human-readable, so if a... [Read More]

  Tags:

  • documentation
  • parameters

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