{"comment":{"url":"https://api.github.com/repos/biojava/biojava/comments/9404203","html_url":"https://github.com/biojava/biojava/commit/45235c07b7f2d056274565a021b86d3ee2c5f76c#commitcomment-9404203","id":9404203,"user":{"login":"dmyersturnbull","id":3979879,"avatar_url":"https://avatars.githubusercontent.com/u/3979879?v=3","gravatar_id":"","url":"https://api.github.com/users/dmyersturnbull","html_url":"https://github.com/dmyersturnbull","followers_url":"https://api.github.com/users/dmyersturnbull/followers","following_url":"https://api.github.com/users/dmyersturnbull/following{/other_user}","gists_url":"https://api.github.com/users/dmyersturnbull/gists{/gist_id}","starred_url":"https://api.github.com/users/dmyersturnbull/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dmyersturnbull/subscriptions","organizations_url":"https://api.github.com/users/dmyersturnbull/orgs","repos_url":"https://api.github.com/users/dmyersturnbull/repos","events_url":"https://api.github.com/users/dmyersturnbull/events{/privacy}","received_events_url":"https://api.github.com/users/dmyersturnbull/received_events","type":"User","site_admin":false},"position":null,"line":null,"path":"","commit_id":"45235c07b7f2d056274565a021b86d3ee2c5f76c","created_at":"2015-01-22T20:12:12Z","updated_at":"2015-01-22T20:12:12Z","body":"@josemduarte I didn't mean that I disagree with the change, only that we should include a line in the release notes mentioning it.\r\n\r\n@andreasprlic I would definitely expect global alignment to penalize gaps on the ends.\r\n\r\nI would expect for local alignment:\r\n - no penalty for gaps on the ends\r\n - gap open penalty for the first indel in a gap\r\n - gap extension penalty for any indel *after the first* in a gap\r\n\r\nFor global, I would expect:\r\n - gap open penalty for the first indel in a gap, including on the ends\r\n - gap extension penalty for any indel *after the first* in a gap, including on the ends\r\n\r\nSo for the global alignment:\r\n```\r\nATGCATGC\r\n---CA-GC\r\n```\r\nI would expect the penalty to be -2 * gop - 2*gep.\r\n\r\nFor the same local alignment, I would expect the penalty to be just -gop.\r\n\r\nAre either of these not the case?"}}