{"action":"created","issue":{"url":"https://api.github.com/repos/vals/umis/issues/3","repository_url":"https://api.github.com/repos/vals/umis","labels_url":"https://api.github.com/repos/vals/umis/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/vals/umis/issues/3/comments","events_url":"https://api.github.com/repos/vals/umis/issues/3/events","html_url":"https://github.com/vals/umis/pull/3","id":134051342,"number":3,"title":"Use regex library and do barcode disambiguation","user":{"login":"roryk","id":414586,"avatar_url":"https://avatars.githubusercontent.com/u/414586?v=3","gravatar_id":"","url":"https://api.github.com/users/roryk","html_url":"https://github.com/roryk","followers_url":"https://api.github.com/users/roryk/followers","following_url":"https://api.github.com/users/roryk/following{/other_user}","gists_url":"https://api.github.com/users/roryk/gists{/gist_id}","starred_url":"https://api.github.com/users/roryk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roryk/subscriptions","organizations_url":"https://api.github.com/users/roryk/orgs","repos_url":"https://api.github.com/users/roryk/repos","events_url":"https://api.github.com/users/roryk/events{/privacy}","received_events_url":"https://api.github.com/users/roryk/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-02-16T17:54:18Z","updated_at":"2016-02-18T00:06:00Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/vals/umis/pulls/3","html_url":"https://github.com/vals/umis/pull/3","diff_url":"https://github.com/vals/umis/pull/3.diff","patch_url":"https://github.com/vals/umis/pull/3.patch"},"body":"Hi Valentine,\r\n\r\nThis pull request has two things, you can reject either one or both.\r\n\r\nThe first is to use the regex library instead of the re library. This allows for syntax to allow mismatches in a regex, so for example:\r\n\r\n```\r\n{\r\n    \"read1\": \"(?P<name>[^\\\\s]+)\\\\n(?P<CB1>\\\\w{8,11})(GAGTGATTGCTTGTGACGCCTT){e<=3}(?P<CB2>\\\\w{8})(?P<MB>\\\\w{6})(.*)\\\\n+(.*)\\\\n(.*)\\\\n\",\r\n    \"read2\": \"(@.*)\\\\n(?P<seq>.*)\\\\n\\\\+(.*)\\\\n(?P<qual>.*)\\\\n\"\r\n}\r\n```\r\n\r\nThe `{e<=3}` syntax allows for 3 or less errors.\r\n\r\nThe second change is to do barcode disambiguation. I abstracted out the writing to either write to barcode files or to stdout depending on if the option is set or not."},"comment":{"url":"https://api.github.com/repos/vals/umis/issues/comments/185467934","html_url":"https://github.com/vals/umis/pull/3#issuecomment-185467934","issue_url":"https://api.github.com/repos/vals/umis/issues/3","id":185467934,"user":{"login":"roryk","id":414586,"avatar_url":"https://avatars.githubusercontent.com/u/414586?v=3","gravatar_id":"","url":"https://api.github.com/users/roryk","html_url":"https://github.com/roryk","followers_url":"https://api.github.com/users/roryk/followers","following_url":"https://api.github.com/users/roryk/following{/other_user}","gists_url":"https://api.github.com/users/roryk/gists{/gist_id}","starred_url":"https://api.github.com/users/roryk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roryk/subscriptions","organizations_url":"https://api.github.com/users/roryk/orgs","repos_url":"https://api.github.com/users/roryk/repos","events_url":"https://api.github.com/users/roryk/events{/privacy}","received_events_url":"https://api.github.com/users/roryk/received_events","type":"User","site_admin":false},"created_at":"2016-02-18T00:06:00Z","updated_at":"2016-02-18T00:06:00Z","body":"I dropped the barcode disambiguation, it was super slow if there were a lot of barcodes. I added an option to keep dual index barcodes separate. There are some preps that have barcode1 and barcode2 but the combination of barcode1 and barcode2 is random, so enumerating and searching through those possibilities for every read takes too long."}}