{"action":"created","issue":{"url":"https://api.github.com/repos/arq5x/bedtools2/issues/441","repository_url":"https://api.github.com/repos/arq5x/bedtools2","labels_url":"https://api.github.com/repos/arq5x/bedtools2/issues/441/labels{/name}","comments_url":"https://api.github.com/repos/arq5x/bedtools2/issues/441/comments","events_url":"https://api.github.com/repos/arq5x/bedtools2/issues/441/events","html_url":"https://github.com/arq5x/bedtools2/issues/441","id":175079062,"number":441,"title":"shuffle -incl in 2.26 is unusably slow when -incl is large","user":{"login":"michael-imbeault","id":7590794,"avatar_url":"https://avatars.githubusercontent.com/u/7590794?v=3","gravatar_id":"","url":"https://api.github.com/users/michael-imbeault","html_url":"https://github.com/michael-imbeault","followers_url":"https://api.github.com/users/michael-imbeault/followers","following_url":"https://api.github.com/users/michael-imbeault/following{/other_user}","gists_url":"https://api.github.com/users/michael-imbeault/gists{/gist_id}","starred_url":"https://api.github.com/users/michael-imbeault/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/michael-imbeault/subscriptions","organizations_url":"https://api.github.com/users/michael-imbeault/orgs","repos_url":"https://api.github.com/users/michael-imbeault/repos","events_url":"https://api.github.com/users/michael-imbeault/events{/privacy}","received_events_url":"https://api.github.com/users/michael-imbeault/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-09-05T14:07:59Z","updated_at":"2016-09-05T21:08:56Z","closed_at":null,"body":"So I finally found time to test out the new shuffle with -incl in 2.26 which takes into account length of intervals... and at least for my use case it is unusably slow - it produces one random interval every 5s or so, and I have thousands of them.\r\n\r\nIt might be related to my -incl being a bed of all transposable elements in the human genome, but still I cannot imagine that this speed is the result of a properly implemented roulette sampling.\r\n\r\nIn the meantime I will keep using the hackish way to do it - I use 2.25 and split my -incl bed in small fragments (20 bp)."},"comment":{"url":"https://api.github.com/repos/arq5x/bedtools2/issues/comments/244811576","html_url":"https://github.com/arq5x/bedtools2/issues/441#issuecomment-244811576","issue_url":"https://api.github.com/repos/arq5x/bedtools2/issues/441","id":244811576,"user":{"login":"arq5x","id":72291,"avatar_url":"https://avatars.githubusercontent.com/u/72291?v=3","gravatar_id":"","url":"https://api.github.com/users/arq5x","html_url":"https://github.com/arq5x","followers_url":"https://api.github.com/users/arq5x/followers","following_url":"https://api.github.com/users/arq5x/following{/other_user}","gists_url":"https://api.github.com/users/arq5x/gists{/gist_id}","starred_url":"https://api.github.com/users/arq5x/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arq5x/subscriptions","organizations_url":"https://api.github.com/users/arq5x/orgs","repos_url":"https://api.github.com/users/arq5x/repos","events_url":"https://api.github.com/users/arq5x/events{/privacy}","received_events_url":"https://api.github.com/users/arq5x/received_events","type":"User","site_admin":false},"created_at":"2016-09-05T21:08:56Z","updated_at":"2016-09-05T21:08:56Z","body":"Nevermind - I can reproduce this. Will try to come up with a more performant approach to roulette sampling."}}
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