{"action":"opened","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/274","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/274/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/274/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/274/events","html_url":"https://github.com/vgteam/vg/issues/274","id":143252194,"number":274,"title":"banded alignment normalization","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":0,"created_at":"2016-03-24T13:54:30Z","updated_at":"2016-03-24T13:54:30Z","closed_at":null,"body":"If reads are aligned using the banded mapper (as they should be for long reads), we may get regions where there are reported indels that should be walking through the reference. This would happen if a band doesn't align or soft clips. We can walk the graph after the fact to normalize perfect matches, or use a local alignment to normalize the alignment. (I prefer the latter idea.)"}}