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

custom ordering of chromosomes #45

Open
rulixxx opened this issue Nov 17, 2021 · 1 comment
Open

custom ordering of chromosomes #45

rulixxx opened this issue Nov 17, 2021 · 1 comment

Comments

@rulixxx
Copy link

rulixxx commented Nov 17, 2021

Hello, having a custom ordering of chromosomes seems to be quite painful at the moment. I've had to overwrite/extend many of the methods from GenomicFeatures and Indexes as they have Base.isless hardcoded into them. This is quite critical for us since we like to work with bioinformatic order instead of lexicographic ordering. We are generating quite large files and just going back to reorder at the end of our analyses would be very painful.

It would be nice to have just one definition of the chromosome order, perhaps in BioGeneric that would get picked up in other modules.

@CiaranOMara
Copy link
Member

Instead of simply using isless we should refactor to use Base.Order.lt and Ordering (see https://docs.julialang.org/en/v1/base/sort/#Alternate-orderings).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

2 participants