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[chore] Update annotation config to use snake case #328

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akotlar opened this issue Oct 24, 2023 · 0 comments
Open

[chore] Update annotation config to use snake case #328

akotlar opened this issue Oct 24, 2023 · 0 comments
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@akotlar
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akotlar commented Oct 24, 2023

Background:

A concise description of why we're pursuing this task.

Currently our YAML config uses a mixture of snake_case and camelCase. See https://github.com/bystrogenomics/bystro/blob/master/config/hg19.clean.yml for an example

Completion Criteria:

What is the goal, and how do we know this task is accomplished?

We move to universally using snake_case for all configured values and update all corresponding variables in the Perl and Python libraries to reflect this, since those are 1:1 in name and we don't want to add remapping complexity.

Implementation Summary

Give enough technical detail for a teammate to understand the proposed solution.

All public attributes in the perl Tracks are potentially configurable from the supplied YAML. See https://github.com/bystrogenomics/bystro/blob/master/perl/lib/Seq/Role/ConfigFromFile.pm#L58, so this will involve converting Perl names to snake_case.

Then we'll need to update https://github.com/bystrogenomics/bystro/blob/master/python/python/bystro/search/utils/annotation.py to go to snake_case for those variables.

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