{"action":"created","issue":{"url":"https://api.github.com/repos/ekg/vg/issues/96","labels_url":"https://api.github.com/repos/ekg/vg/issues/96/labels{/name}","comments_url":"https://api.github.com/repos/ekg/vg/issues/96/comments","events_url":"https://api.github.com/repos/ekg/vg/issues/96/events","html_url":"https://github.com/ekg/vg/pull/96","id":105250070,"number":96,"title":"Add vg pileup command to transpose read alignments to alignment columns","user":{"login":"glennhickey","id":901102,"avatar_url":"https://avatars.githubusercontent.com/u/901102?v=3","gravatar_id":"","url":"https://api.github.com/users/glennhickey","html_url":"https://github.com/glennhickey","followers_url":"https://api.github.com/users/glennhickey/followers","following_url":"https://api.github.com/users/glennhickey/following{/other_user}","gists_url":"https://api.github.com/users/glennhickey/gists{/gist_id}","starred_url":"https://api.github.com/users/glennhickey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/glennhickey/subscriptions","organizations_url":"https://api.github.com/users/glennhickey/orgs","repos_url":"https://api.github.com/users/glennhickey/repos","events_url":"https://api.github.com/users/glennhickey/events{/privacy}","received_events_url":"https://api.github.com/users/glennhickey/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-09-07T17:25:16Z","updated_at":"2015-09-10T13:55:50Z","closed_at":"2015-09-10T13:55:50Z","pull_request":{"url":"https://api.github.com/repos/ekg/vg/pulls/96","html_url":"https://github.com/ekg/vg/pull/96","diff_url":"https://github.com/ekg/vg/pull/96.diff","patch_url":"https://github.com/ekg/vg/pull/96.patch"},"body":"I'm cobbling together a rudimentary vg variant caller for the purposes of evaluating graph construction and mapping methods in our bakeoff.  This PR is the first step for this, and adds basic functionality similar to samtools pileup:\r\n\r\n* NodePileup record added to protobuf defs\r\n* vg pileup command added to convert GAM to pileup format\r\n* vg view changed to support pileups\r\n* vg view changed to support json input of GAMs (only change that affects existing functionality)\r\n* simple pileup test added. \r\n\r\n "},"comment":{"url":"https://api.github.com/repos/ekg/vg/issues/comments/139241590","html_url":"https://github.com/ekg/vg/pull/96#issuecomment-139241590","issue_url":"https://api.github.com/repos/ekg/vg/issues/96","id":139241590,"user":{"login":"glennhickey","id":901102,"avatar_url":"https://avatars.githubusercontent.com/u/901102?v=3","gravatar_id":"","url":"https://api.github.com/users/glennhickey","html_url":"https://github.com/glennhickey","followers_url":"https://api.github.com/users/glennhickey/followers","following_url":"https://api.github.com/users/glennhickey/following{/other_user}","gists_url":"https://api.github.com/users/glennhickey/gists{/gist_id}","starred_url":"https://api.github.com/users/glennhickey/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/glennhickey/subscriptions","organizations_url":"https://api.github.com/users/glennhickey/orgs","repos_url":"https://api.github.com/users/glennhickey/repos","events_url":"https://api.github.com/users/glennhickey/events{/privacy}","received_events_url":"https://api.github.com/users/glennhickey/received_events","type":"User","site_admin":false},"created_at":"2015-09-10T13:55:50Z","updated_at":"2015-09-10T13:55:50Z","body":"Actually, let's wait until this is more mature (ie been used in next iteration of mapping bakeoff), before merging.  Worried I'll have to play around with the pileup logic / structure more than I'd expected in the meantime..  Will send updated PR later.    "}}