{"action":"created","issue":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/50","labels_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/50/labels{/name}","comments_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/50/comments","events_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/50/events","html_url":"https://github.com/BioJulia/Bio.jl/pull/50","id":70946236,"number":50,"title":"WIP: BED Parser","user":{"login":"dcjones","id":210361,"avatar_url":"https://avatars.githubusercontent.com/u/210361?v=3","gravatar_id":"","url":"https://api.github.com/users/dcjones","html_url":"https://github.com/dcjones","followers_url":"https://api.github.com/users/dcjones/followers","following_url":"https://api.github.com/users/dcjones/following{/other_user}","gists_url":"https://api.github.com/users/dcjones/gists{/gist_id}","starred_url":"https://api.github.com/users/dcjones/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dcjones/subscriptions","organizations_url":"https://api.github.com/users/dcjones/orgs","repos_url":"https://api.github.com/users/dcjones/repos","events_url":"https://api.github.com/users/dcjones/events{/privacy}","received_events_url":"https://api.github.com/users/dcjones/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":13,"created_at":"2015-04-25T18:08:23Z","updated_at":"2015-05-09T03:21:43Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/pulls/50","html_url":"https://github.com/BioJulia/Bio.jl/pull/50","diff_url":"https://github.com/BioJulia/Bio.jl/pull/50.diff","patch_url":"https://github.com/BioJulia/Bio.jl/pull/50.patch"},"body":"Here's a parser for BED format. It's not really tested yet. I need to collect BED specimens and build test cases, so there are almost certainly still bugs. Note: all the commits are because this is branched from by `intervals` branch, which is branched from my `io` branch. So don't be alarmed. :smile: \r\n\r\nThe one file I tested it on had 10k 6-column entries. That parsed in 0.016 seconds, so perf seems pretty solid.\r\n\r\nBy the way, one thing I'm pretty excited about: if you have two sorted BED files (or eventually any kind of file that stores intervals), you can iterate over intersections without even reading either into memory like:\r\n\r\n```julia\r\nintersect(read(\"file1.bed\", BED), read(\"file2.bed\", BED))\r\n```"},"comment":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/comments/100417696","html_url":"https://github.com/BioJulia/Bio.jl/pull/50#issuecomment-100417696","issue_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/50","id":100417696,"user":{"login":"dcjones","id":210361,"avatar_url":"https://avatars.githubusercontent.com/u/210361?v=3","gravatar_id":"","url":"https://api.github.com/users/dcjones","html_url":"https://github.com/dcjones","followers_url":"https://api.github.com/users/dcjones/followers","following_url":"https://api.github.com/users/dcjones/following{/other_user}","gists_url":"https://api.github.com/users/dcjones/gists{/gist_id}","starred_url":"https://api.github.com/users/dcjones/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dcjones/subscriptions","organizations_url":"https://api.github.com/users/dcjones/orgs","repos_url":"https://api.github.com/users/dcjones/repos","events_url":"https://api.github.com/users/dcjones/events{/privacy}","received_events_url":"https://api.github.com/users/dcjones/received_events","type":"User","site_admin":false},"created_at":"2015-05-09T03:21:43Z","updated_at":"2015-05-09T03:21:43Z","body":"I agree, it should eventually be split into a separate package, but like you say, I'm prioritizing parsers and docs for now."}}