{"action":"closed","issue":{"url":"https://api.github.com/repos/a-ludi/djunctor/issues/31","repository_url":"https://api.github.com/repos/a-ludi/djunctor","labels_url":"https://api.github.com/repos/a-ludi/djunctor/issues/31/labels{/name}","comments_url":"https://api.github.com/repos/a-ludi/djunctor/issues/31/comments","events_url":"https://api.github.com/repos/a-ludi/djunctor/issues/31/events","html_url":"https://github.com/a-ludi/djunctor/issues/31","id":326448856,"node_id":"MDU6SXNzdWUzMjY0NDg4NTY=","number":31,"title":"Avoid using two LAS files for the same alignment (`-C` option)","user":{"login":"a-ludi","id":1200170,"node_id":"MDQ6VXNlcjEyMDAxNzA=","avatar_url":"https://avatars2.githubusercontent.com/u/1200170?v=4","gravatar_id":"","url":"https://api.github.com/users/a-ludi","html_url":"https://github.com/a-ludi","followers_url":"https://api.github.com/users/a-ludi/followers","following_url":"https://api.github.com/users/a-ludi/following{/other_user}","gists_url":"https://api.github.com/users/a-ludi/gists{/gist_id}","starred_url":"https://api.github.com/users/a-ludi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/a-ludi/subscriptions","organizations_url":"https://api.github.com/users/a-ludi/orgs","repos_url":"https://api.github.com/users/a-ludi/repos","events_url":"https://api.github.com/users/a-ludi/events{/privacy}","received_events_url":"https://api.github.com/users/a-ludi/received_events","type":"User","site_admin":false},"labels":[{"id":872395039,"node_id":"MDU6TGFiZWw4NzIzOTUwMzk=","url":"https://api.github.com/repos/a-ludi/djunctor/labels/enhancement","name":"enhancement","color":"a2eeef","default":true}],"state":"closed","locked":false,"assignee":{"login":"a-ludi","id":1200170,"node_id":"MDQ6VXNlcjEyMDAxNzA=","avatar_url":"https://avatars2.githubusercontent.com/u/1200170?v=4","gravatar_id":"","url":"https://api.github.com/users/a-ludi","html_url":"https://github.com/a-ludi","followers_url":"https://api.github.com/users/a-ludi/followers","following_url":"https://api.github.com/users/a-ludi/following{/other_user}","gists_url":"https://api.github.com/users/a-ludi/gists{/gist_id}","starred_url":"https://api.github.com/users/a-ludi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/a-ludi/subscriptions","organizations_url":"https://api.github.com/users/a-ludi/orgs","repos_url":"https://api.github.com/users/a-ludi/repos","events_url":"https://api.github.com/users/a-ludi/events{/privacy}","received_events_url":"https://api.github.com/users/a-ludi/received_events","type":"User","site_admin":false},"assignees":[{"login":"a-ludi","id":1200170,"node_id":"MDQ6VXNlcjEyMDAxNzA=","avatar_url":"https://avatars2.githubusercontent.com/u/1200170?v=4","gravatar_id":"","url":"https://api.github.com/users/a-ludi","html_url":"https://github.com/a-ludi","followers_url":"https://api.github.com/users/a-ludi/followers","following_url":"https://api.github.com/users/a-ludi/following{/other_user}","gists_url":"https://api.github.com/users/a-ludi/gists{/gist_id}","starred_url":"https://api.github.com/users/a-ludi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/a-ludi/subscriptions","organizations_url":"https://api.github.com/users/a-ludi/orgs","repos_url":"https://api.github.com/users/a-ludi/repos","events_url":"https://api.github.com/users/a-ludi/events{/privacy}","received_events_url":"https://api.github.com/users/a-ludi/received_events","type":"User","site_admin":false}],"milestone":null,"comments":0,"created_at":"2018-05-25T09:31:16Z","updated_at":"2018-06-13T07:44:55Z","closed_at":"2018-06-13T07:44:55Z","author_association":"OWNER","body":"Using the `-C` option of `damapper` produces to two LAS files `[B-reads].[A-reads].las` and `[A-reads].[B-reads].las`. Currently, both files are used for different purposes and a mapping between alignment chains of both must be made. This seems to generate unnecessary complexity, thus opening doors for errors.\r\n\r\n### Tasks\r\n- [x] Why are both files being used?\r\n- [x] Refactor the whole code base as to avoid using both. A starting point is to remove `djunctor.djunctor.AlignmentContainer`."}}
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