{"action":"opened","issue":{"url":"https://api.github.com/repos/barricklab/breseq/issues/84","labels_url":"https://api.github.com/repos/barricklab/breseq/issues/84/labels{/name}","comments_url":"https://api.github.com/repos/barricklab/breseq/issues/84/comments","events_url":"https://api.github.com/repos/barricklab/breseq/issues/84/events","html_url":"https://github.com/barricklab/breseq/issues/84","id":109936052,"number":84,"title":"Overlapping mobile_element / repeat_sequence causing transposon to not be called","user":{"login":"jeffreybarrick","id":6777876,"avatar_url":"https://avatars.githubusercontent.com/u/6777876?v=3","gravatar_id":"","url":"https://api.github.com/users/jeffreybarrick","html_url":"https://github.com/jeffreybarrick","followers_url":"https://api.github.com/users/jeffreybarrick/followers","following_url":"https://api.github.com/users/jeffreybarrick/following{/other_user}","gists_url":"https://api.github.com/users/jeffreybarrick/gists{/gist_id}","starred_url":"https://api.github.com/users/jeffreybarrick/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jeffreybarrick/subscriptions","organizations_url":"https://api.github.com/users/jeffreybarrick/orgs","repos_url":"https://api.github.com/users/jeffreybarrick/repos","events_url":"https://api.github.com/users/jeffreybarrick/events{/privacy}","received_events_url":"https://api.github.com/users/jeffreybarrick/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-10-06T05:06:54Z","updated_at":"2015-10-06T05:06:54Z","closed_at":null,"body":"breseq is confused by transposons annotated as 'mobile_element' with 'repeat_region' for the terminal repeats. It should favor the mobile_element so that it can call the transposon insertions correctly from junctions and only use repeat regions as a backup. Need to implement this at the level of code that looks for the overlapping elements. This is the bug that prevents ISMapper from finding the Acinetobacter transposon insertions."}}