{"action":"created","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/236","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/236/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/236/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/236/events","html_url":"https://github.com/vgteam/vg/issues/236","id":136368442,"number":236,"title":"deconstruct shouldn't need to take a reference FASTA file","user":{"login":"ekg","id":145425,"avatar_url":"https://avatars.githubusercontent.com/u/145425?v=3","gravatar_id":"","url":"https://api.github.com/users/ekg","html_url":"https://github.com/ekg","followers_url":"https://api.github.com/users/ekg/followers","following_url":"https://api.github.com/users/ekg/following{/other_user}","gists_url":"https://api.github.com/users/ekg/gists{/gist_id}","starred_url":"https://api.github.com/users/ekg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekg/subscriptions","organizations_url":"https://api.github.com/users/ekg/orgs","repos_url":"https://api.github.com/users/ekg/repos","events_url":"https://api.github.com/users/ekg/events{/privacy}","received_events_url":"https://api.github.com/users/ekg/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-02-25T12:01:40Z","updated_at":"2016-02-25T12:04:50Z","closed_at":null,"body":"It would be nice to do this:\r\n\r\n```\r\n➜  test git:(master) ✗ vg msga -f x.fa | vg deconstruct -p path - -o x.vcf\r\nError: A reference is needed for projection into vcf.\r\n```\r\n\r\nThe reference path is embedded in the input, so maybe we could pull it directly out of the graph rather than use an external file? For instance, I may not have a FASTA file at all for any of the paths in my graph."},"comment":{"url":"https://api.github.com/repos/vgteam/vg/issues/comments/188755159","html_url":"https://github.com/vgteam/vg/issues/236#issuecomment-188755159","issue_url":"https://api.github.com/repos/vgteam/vg/issues/236","id":188755159,"user":{"login":"edawson","id":2595153,"avatar_url":"https://avatars.githubusercontent.com/u/2595153?v=3","gravatar_id":"","url":"https://api.github.com/users/edawson","html_url":"https://github.com/edawson","followers_url":"https://api.github.com/users/edawson/followers","following_url":"https://api.github.com/users/edawson/following{/other_user}","gists_url":"https://api.github.com/users/edawson/gists{/gist_id}","starred_url":"https://api.github.com/users/edawson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edawson/subscriptions","organizations_url":"https://api.github.com/users/edawson/orgs","repos_url":"https://api.github.com/users/edawson/repos","events_url":"https://api.github.com/users/edawson/events{/privacy}","received_events_url":"https://api.github.com/users/edawson/received_events","type":"User","site_admin":false},"created_at":"2016-02-25T12:04:50Z","updated_at":"2016-02-25T12:04:50Z","body":"There are some other issues with deconstruct as well:\r\n1. Streaming input is probably not implemented (at least in an obvious way).\r\n2. It doesn't like reversals in the graph.\r\n3. Its interface (especially the help message) is pretty broken.\r\n\r\nI will put it on my todo list to patch these things up."}}