Faith Okamoto | Science Code

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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
Format your code

April 2025
By Faith Okamoto
Posted on April 26, 2025

I’m running out of time for this month’s published-code-critique. Luckily, Nature’s front page had this gem: a paper literally referring back to the days of Mendel1! [Read More]
Tags:
- published-code-critique
- style
Directory READMEs

From the list of "things I wish other people did"
By Faith Okamoto
Posted on April 19, 2025

I’ve mentioned that I make a README as the first file in any new project directory. Here, I’ll detail what goes in this README. [Read More]
Tags:
Magic numbers in plotting

Abracadabra, make a graph!
By Faith Okamoto
Posted on April 5, 2025

I’ve just started a class on making scientific plots so I’ll cover a common phenomenon: magic numbers. [Read More]
Tags:
- style
- plots

Parameters implying other parameters

But what does that mean?

Documenting options

What choices do I have?

Format your code

April 2025

Directory READMEs

From the list of "things I wish other people did"

Magic numbers in plotting

Abracadabra, make a graph!