{"action":"opened","issue":{"url":"https://api.github.com/repos/Martinsos/edlib/issues/116","repository_url":"https://api.github.com/repos/Martinsos/edlib","labels_url":"https://api.github.com/repos/Martinsos/edlib/issues/116/labels{/name}","comments_url":"https://api.github.com/repos/Martinsos/edlib/issues/116/comments","events_url":"https://api.github.com/repos/Martinsos/edlib/issues/116/events","html_url":"https://github.com/Martinsos/edlib/issues/116","id":312335130,"number":116,"title":"request: scoring of indels","user":{"login":"romain22","id":27407711,"avatar_url":"https://avatars0.githubusercontent.com/u/27407711?v=4","gravatar_id":"","url":"https://api.github.com/users/romain22","html_url":"https://github.com/romain22","followers_url":"https://api.github.com/users/romain22/followers","following_url":"https://api.github.com/users/romain22/following{/other_user}","gists_url":"https://api.github.com/users/romain22/gists{/gist_id}","starred_url":"https://api.github.com/users/romain22/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/romain22/subscriptions","organizations_url":"https://api.github.com/users/romain22/orgs","repos_url":"https://api.github.com/users/romain22/repos","events_url":"https://api.github.com/users/romain22/events{/privacy}","received_events_url":"https://api.github.com/users/romain22/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-04-08T19:55:22Z","updated_at":"2018-04-08T19:55:22Z","closed_at":null,"author_association":"NONE","body":"it is not strictly speaking an issue, more like a request for further improvements.\r\n\r\nUsing biological data (DNA,RNA or protein sequences), one usually consider that the deletion of n adjacent characters is the result of a unique evolutionary event (same apply for insertion).\r\n\r\nThe problem is that edlib will score n edits for the deletion/insertion of n adjacent characters.\r\nFor instance, in this case edlib will return an editDistance of 3:\r\nTAGCGTAGCTAGCCTATTATCG\r\nTAGCGTAGCTA --- TATTATCG\r\n... while the most parsimonious answer is 1 (i.e. 1 change, consisting of the insertion/deletion of GCC). \r\nnb: I believe this reasoning is correct for the comparison of any kind of string.\r\n\r\nSo, I was wondering if it would be possible to add on option to edlib.align() to score 1 edit for any insertion/deletion of n adjacent characters.\r\n\r\nthanks.\r\n"}}
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