{"action":"created","issue":{"url":"https://api.github.com/repos/torognes/vsearch/issues/147","labels_url":"https://api.github.com/repos/torognes/vsearch/issues/147/labels{/name}","comments_url":"https://api.github.com/repos/torognes/vsearch/issues/147/comments","events_url":"https://api.github.com/repos/torognes/vsearch/issues/147/events","html_url":"https://github.com/torognes/vsearch/issues/147","id":118580150,"number":147,"title":"Letter case not preserved","user":{"login":"torognes","id":2765754,"avatar_url":"https://avatars.githubusercontent.com/u/2765754?v=3","gravatar_id":"","url":"https://api.github.com/users/torognes","html_url":"https://github.com/torognes","followers_url":"https://api.github.com/users/torognes/followers","following_url":"https://api.github.com/users/torognes/following{/other_user}","gists_url":"https://api.github.com/users/torognes/gists{/gist_id}","starred_url":"https://api.github.com/users/torognes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/torognes/subscriptions","organizations_url":"https://api.github.com/users/torognes/orgs","repos_url":"https://api.github.com/users/torognes/repos","events_url":"https://api.github.com/users/torognes/events{/privacy}","received_events_url":"https://api.github.com/users/torognes/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/torognes/vsearch/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-11-24T10:45:29Z","updated_at":"2015-12-07T13:51:15Z","closed_at":null,"body":"A user reported that vsearch and usearch7 does not behave identical regarding the letter case of sequences when mixed case was used in the input. The output from the command below was different from that of usearch7.\r\n\r\n`vsearch -cluster_fast in -msaout v.out -qmask none -dbmask none -id 0.96 -self -minsl 0.9 -query_cov 0.9 -target_cov 0.9 -maxaccepts 0 -maxrejects 0 -gapopen 3I/0L`\r\n\r\nSee details on the VSEARCH Forum: https://groups.google.com/d/msgid/vsearch-forum/c8d34136-2388-4e54-9e74-513f533efada%40googlegroups.com\r\n"},"comment":{"url":"https://api.github.com/repos/torognes/vsearch/issues/comments/162529160","html_url":"https://github.com/torognes/vsearch/issues/147#issuecomment-162529160","issue_url":"https://api.github.com/repos/torognes/vsearch/issues/147","id":162529160,"user":{"login":"torognes","id":2765754,"avatar_url":"https://avatars.githubusercontent.com/u/2765754?v=3","gravatar_id":"","url":"https://api.github.com/users/torognes","html_url":"https://github.com/torognes","followers_url":"https://api.github.com/users/torognes/followers","following_url":"https://api.github.com/users/torognes/following{/other_user}","gists_url":"https://api.github.com/users/torognes/gists{/gist_id}","starred_url":"https://api.github.com/users/torognes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/torognes/subscriptions","organizations_url":"https://api.github.com/users/torognes/orgs","repos_url":"https://api.github.com/users/torognes/repos","events_url":"https://api.github.com/users/torognes/events{/privacy}","received_events_url":"https://api.github.com/users/torognes/received_events","type":"User","site_admin":false},"created_at":"2015-12-07T13:51:15Z","updated_at":"2015-12-07T13:51:15Z","body":"I am not sure about what to do here. We can pass the case of the letters though unmodified, that's no problem. However, the behaviour of usearch regarding masking and clustering is confusing. The actual behaviour seems to be different from the documentation and the defaults are non-standard, as described earlier. I do not know if we should try to be as similar as possible, if we should just ignore masking when clustering alltogether, or if we should try to implement it properly as a user would expect. I guess masking is rarely used intentionally when clustering. Masking is supposed just to matter when extracting indexing words. Any opinions?"}}