search

zaeleus / noodles

Bioinformatics I/O libraries in Rust
MIT License
477 stars 53 forks source link

About method names of `noodles_sam::alignment::record::Flags` #253

Closed Crispy13 closed 4 months ago

Crispy13 commented 4 months ago

Hi.

How would you feel about renaming flag getter names according to https://broadinstitute.github.io/picard/explain-flags.html?

For example, is_segmented() will be renamed to is_paired().

I think it would be good for noob bioinformaticians like me.

Also, do you have any rules for contributing this repo? If so, I may try to pull request a little for some functions in htsjdk(SamReadGroup, unclipped_pos, etc.)

Thanks

zaeleus commented 4 months ago

noodles uses the terminology defined by the SAM format specification. See § 1.4.2 "The alignment section: mandatory fields: FLAGS" (2023-05-24) for flag descriptions.

It is not a design goal of noodles to copy or follow the API of existing libraries. It should provide a foundation to allow you to achieve writing those functions in your own applications. If you have questions on the availability of certain features, do feel free to start a new discussion.

Crispy13 commented 4 months ago

Ah, I see. But some libraries (htsjdk, pysam, rust-htslib) seems to use the names in the site I linked.

Or It may be good to write other names on doc comments of the methods.