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href=\"https://github.com/recursion-ninja\"><img src=\"https://avatars3.githubusercontent.com/u/6666514?v=3\" align=\"left\" width=\"96\" height=\"96\" hspace=\"10\"></img></a> **Issue by [recursion-ninja](https://github.com/recursion-ninja)**\r\n_Tuesday Mar 28, 2017 at 20:57 GMT_\r\n_Originally opened as https://github.com/ima-hima/PCG/issues/15_\r\n\r\n----\r\n\r\nEnsure that sequential align preserves \"alignment\" invariants:\r\n\r\n - [ ] Preserve all the bases from the input sequences.\r\n\r\n - [ ] Only add gap characters to input sequences.\r\n\r\n - [ ] Don't get accidentally switched.\r\n\r\nAdditionally:\r\n\r\n - [ ] Get correct alignment costs (currently they're always 0).\r\n\r\n - [ ] Get valid input/output pairs, preferably more than one, for future validation after updates.\r\n\r\n - [ ] Add support for large alphabets (i.e. provided bit vector library).\r\n\r\n - [ ] Continue to refactor/rename/document.\r\n"},"comment":{"url":"https://api.github.com/repos/amnh/PCG/issues/comments/486621275","html_url":"https://github.com/amnh/PCG/issues/15#issuecomment-486621275","issue_url":"https://api.github.com/repos/amnh/PCG/issues/15","id":486621275,"node_id":"MDEyOklzc3VlQ29tbWVudDQ4NjYyMTI3NQ==","user":{"login":"recursion-ninja","id":6666514,"node_id":"MDQ6VXNlcjY2NjY1MTQ=","avatar_url":"https://avatars0.githubusercontent.com/u/6666514?v=4","gravatar_id":"","url":"https://api.github.com/users/recursion-ninja","html_url":"https://github.com/recursion-ninja","followers_url":"https://api.github.com/users/recursion-ninja/followers","following_url":"https://api.github.com/users/recursion-ninja/following{/other_user}","gists_url":"https://api.github.com/users/recursion-ninja/gists{/gist_id}","starred_url":"https://api.github.com/users/recursion-ninja/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/recursion-ninja/subscriptions","organizations_url":"https://api.github.com/users/recursion-ninja/orgs","repos_url":"https://api.github.com/users/recursion-ninja/repos","events_url":"https://api.github.com/users/recursion-ninja/events{/privacy}","received_events_url":"https://api.github.com/users/recursion-ninja/received_events","type":"User","site_admin":false},"created_at":"2019-04-25T10:42:17Z","updated_at":"2019-04-25T10:42:17Z","author_association":"COLLABORATOR","body":"Closing as beyond the scope of PCG. Sequential Alignment has been relegated to the `prototype` zone."}}
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