Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add empty! in read! method #18

Merged
merged 2 commits into from
Apr 5, 2024
Merged

Conversation

jonathanBieler
Copy link
Contributor

Most BioJulia packages use

reader = X.Reader(GzipDecompressorStream(open(file)))
record = X.Record()
read!(reader, record)

to read in-place, while GFF3 requires to call empty! before reading. This change makes it follow the same interface as the rest of the ecosystem.

I tried to reproduce the issue I ran into when I was not calling empty! but all the test files where already working. I still kept the additional tests.

Problematic file was this one :

https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.basic.annotation.gff3.gz
https://www.gencodegenes.org/human/release_26.html

But it now works.

Types of changes

This PR implements the following changes:
(Please tick any or all of the following that are applicable)

  • ✨ New feature (A non-breaking change which adds functionality).
  • 🐛 Bug fix (A non-breaking change, which fixes an issue).
  • 💥 Breaking change (fix or feature that would cause existing functionality to change).

Copy link
Member

@kescobo kescobo left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM! Thanks for taking this on 👍

@kescobo kescobo added the enhancement New feature or request label Oct 23, 2023
@kescobo
Copy link
Member

kescobo commented Oct 23, 2023

Segfault on nightly seems unrelated ?

@jakobnissen
Copy link
Member

Looks good to me too, thanks for doing this!

@jakobnissen jakobnissen merged commit 03e3b79 into BioJulia:develop Apr 5, 2024
14 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants