{"action":"created","issue":{"url":"https://api.github.com/repos/GMOD/jbrowse/issues/317","repository_url":"https://api.github.com/repos/GMOD/jbrowse","labels_url":"https://api.github.com/repos/GMOD/jbrowse/issues/317/labels{/name}","comments_url":"https://api.github.com/repos/GMOD/jbrowse/issues/317/comments","events_url":"https://api.github.com/repos/GMOD/jbrowse/issues/317/events","html_url":"https://github.com/GMOD/jbrowse/issues/317","id":18012483,"number":317,"title":"Support refseqs stored as faidx-indexed fasta files","user":{"login":"benwbooth","id":75972,"avatar_url":"https://avatars.githubusercontent.com/u/75972?v=3","gravatar_id":"","url":"https://api.github.com/users/benwbooth","html_url":"https://github.com/benwbooth","followers_url":"https://api.github.com/users/benwbooth/followers","following_url":"https://api.github.com/users/benwbooth/following{/other_user}","gists_url":"https://api.github.com/users/benwbooth/gists{/gist_id}","starred_url":"https://api.github.com/users/benwbooth/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benwbooth/subscriptions","organizations_url":"https://api.github.com/users/benwbooth/orgs","repos_url":"https://api.github.com/users/benwbooth/repos","events_url":"https://api.github.com/users/benwbooth/events{/privacy}","received_events_url":"https://api.github.com/users/benwbooth/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/GMOD/jbrowse/labels/feature","name":"feature","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/GMOD/jbrowse/milestones/2","html_url":"https://github.com/GMOD/jbrowse/milestones/Release%202.0.0","labels_url":"https://api.github.com/repos/GMOD/jbrowse/milestones/2/labels","id":93862,"number":2,"title":"Release 2.0.0","description":"","creator":{"login":"rbuels","id":73749,"avatar_url":"https://avatars.githubusercontent.com/u/73749?v=3","gravatar_id":"","url":"https://api.github.com/users/rbuels","html_url":"https://github.com/rbuels","followers_url":"https://api.github.com/users/rbuels/followers","following_url":"https://api.github.com/users/rbuels/following{/other_user}","gists_url":"https://api.github.com/users/rbuels/gists{/gist_id}","starred_url":"https://api.github.com/users/rbuels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rbuels/subscriptions","organizations_url":"https://api.github.com/users/rbuels/orgs","repos_url":"https://api.github.com/users/rbuels/repos","events_url":"https://api.github.com/users/rbuels/events{/privacy}","received_events_url":"https://api.github.com/users/rbuels/received_events","type":"User","site_admin":false},"open_issues":40,"closed_issues":22,"state":"open","created_at":"2012-03-08T18:22:44Z","updated_at":"2016-06-09T21:59:53Z","due_on":null,"closed_at":null},"comments":17,"created_at":"2013-08-13T18:28:11Z","updated_at":"2016-08-10T15:14:50Z","closed_at":null,"body":"samtools has a faidx option that can produce an index for a fasta file, as documented here:\n\nhttp://samtools.sourceforge.net/samtools.shtml\n\nIt would be really cool if JBrowse could read refseqs in plain fasta format using these index files. That would make it unnecessary to run the prepare-refseqs.pl script, and you could just have a single fasta file and a .fai index file instead of a bunch of directories and files to store your refseqs."},"comment":{"url":"https://api.github.com/repos/GMOD/jbrowse/issues/comments/238899263","html_url":"https://github.com/GMOD/jbrowse/issues/317#issuecomment-238899263","issue_url":"https://api.github.com/repos/GMOD/jbrowse/issues/317","id":238899263,"user":{"login":"cmdcolin","id":6511937,"avatar_url":"https://avatars.githubusercontent.com/u/6511937?v=3","gravatar_id":"","url":"https://api.github.com/users/cmdcolin","html_url":"https://github.com/cmdcolin","followers_url":"https://api.github.com/users/cmdcolin/followers","following_url":"https://api.github.com/users/cmdcolin/following{/other_user}","gists_url":"https://api.github.com/users/cmdcolin/gists{/gist_id}","starred_url":"https://api.github.com/users/cmdcolin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmdcolin/subscriptions","organizations_url":"https://api.github.com/users/cmdcolin/orgs","repos_url":"https://api.github.com/users/cmdcolin/repos","events_url":"https://api.github.com/users/cmdcolin/events{/privacy}","received_events_url":"https://api.github.com/users/cmdcolin/received_events","type":"User","site_admin":false},"created_at":"2016-08-10T15:14:50Z","updated_at":"2016-08-10T15:14:50Z","body":"@keiranmraine actually neither. the only thing that is implemented to my knowledge is uncompressed indexed fasta, so basically just a regular fasta file that has been indexed, e.g. samtools faidx regular_fasta.fa\r\n\r\nNote that the twobit pull request https://github.com/GMOD/jbrowse/pull/759 provides optimal compression and could be tested too. It works great in my experience with it\r\n"}}
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