{"action":"closed","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/1438","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/1438/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/1438/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/1438/events","html_url":"https://github.com/vgteam/vg/issues/1438","id":296224992,"number":1438,"title":"vg view -d error post vg find, still produces dot file but seems wrong","user":{"login":"wheaton5","id":4810406,"avatar_url":"https://avatars1.githubusercontent.com/u/4810406?v=4","gravatar_id":"","url":"https://api.github.com/users/wheaton5","html_url":"https://github.com/wheaton5","followers_url":"https://api.github.com/users/wheaton5/followers","following_url":"https://api.github.com/users/wheaton5/following{/other_user}","gists_url":"https://api.github.com/users/wheaton5/gists{/gist_id}","starred_url":"https://api.github.com/users/wheaton5/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wheaton5/subscriptions","organizations_url":"https://api.github.com/users/wheaton5/orgs","repos_url":"https://api.github.com/users/wheaton5/repos","events_url":"https://api.github.com/users/wheaton5/events{/privacy}","received_events_url":"https://api.github.com/users/wheaton5/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-02-11T21:00:05Z","updated_at":"2018-02-12T17:22:39Z","closed_at":"2018-02-12T17:22:39Z","author_association":"NONE","body":"https://drive.google.com/open?id=1Ix6YM63MLzLWonbwGcGjgosuxlIuHC08\r\n\r\nxg and command to produce error available on my google drive at that link.\r\n\r\nerror is\r\ngraph invalid: edge index=0 (1925->1926) cannot find node (from) 1925\r\n[vg view] warning: graph is invalid!\r\n\r\nthis does not occur if you do vg view -d reference.vg (file also provided)\r\n\r\nThe dot provided by the command that errors does have indels but does not have snps which should be present and seem to be present in the vg view -d reference.vg dot file via inspection of the text (I cannot produce a picture of the resulting large graph).\r\n\r\nWhat I am mostly interested in is inspecting some regions that are fully diverged and seeing if the vg augment (or vg mod) commands I have tried have added some fermi contigs that span these regions. I tried it on one such region but it looked linear + indels.\r\n\r\n"}}
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