Register BioJulia types ?
Open
Nobody has claimed this yet.
- Dominant language
- Julia
- Stars
- 228
- Forks
- 81
- Avg merge
- 1d 29m
- Merged PRs (30d)
- 1
Description
Hi, I'd like to register some of the common file types used in bioinformatics. But I'd like to make sure it would be ok to take this extensions for FileIO before doing the work. All these files are very common in bioinformatics.
- .bed https://en.wikipedia.org/wiki/BED_(file_format) : the extension doesn't seem to have other common use, but there's no magic bytes for it (plain text with loose standard).
- .vcf (Variant Call Format): This one is ambiguous with "Virtual Contact File", but the file is supposed to always start with "##fileformat=VCF" (and this is enforced in our Julia loader) so I think we can add the magic argument for it.
- .fasta/fastq : no ambiguity for these (but no magic bytes either).
- GFF3 : no ambiguity (might be able to detect the header but not totally sure).
Would those be ok to add ? Thanks.
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No source file or test is named. Start by checking FileIO's existing registration and magic-detection conventions, then confirm how Julia loaders handle BED, VCF, FASTA/FASTQ, and GFF3. Done means an agreed registration approach for the listed extensions, including the VCF header ambiguity.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- julia
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100