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BioJulia / Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
http://biojulia.dev
MIT License
261 stars 63 forks source link

Module files should start with uppercase #46

Closed prcastro closed 9 years ago

prcastro commented 9 years ago

Following conventions in other Julia packages, I propose we rename all module files and folders to start with uppercase (e.g. src/seq/seq.jl to src/Seq/Seq.jl).

dcjones commented 9 years ago

This is probably a good idea, though I'm slightly dreading rebasing on that change on my silly case insensitive filesystem.

blahah commented 9 years ago

Can we build this and any other similar issues into a styleguide?

prcastro commented 9 years ago

That's a great idea. Maybe introduce a CONTRIBUTING.md file with this content on the root dir of the project and remove it from the Wiki (since it's kind of hard to find it there).

TransGirlCodes commented 9 years ago

Has this been done and ready to close?

dcjones commented 9 years ago

This is #63, which hasn't been merged. I want to selfishly request that this waits until #51 is merged, because I'm afraid it will be a pain to rebase on this. :smile:

TransGirlCodes commented 9 years ago

That's fine by me! :) I just took a brief look at the bigbed branch - a lot to read and understand at first glance, but I like the look of the file buffer code in src/ . IF I understand it correctly, it can either contain a memory mapped Mmap.mmap, or a file stream, and incrementally read in data to a buffer. This strikes me as an incredibly useful thing for other areas too - I imagine a butt load of population genetics data from simulation for example, or big tables of polymorphism data.

dcjones commented 9 years ago

Yeah the intent is to abstract over reading all at once, incrementally, or mmaping and use that for all the parsers. I'd like to add support for reading from http too.

prcastro commented 9 years ago

Solved by #97