{"action":"created","issue":{"url":"https://api.github.com/repos/marcelm/cutadapt/issues/128","labels_url":"https://api.github.com/repos/marcelm/cutadapt/issues/128/labels{/name}","comments_url":"https://api.github.com/repos/marcelm/cutadapt/issues/128/comments","events_url":"https://api.github.com/repos/marcelm/cutadapt/issues/128/events","html_url":"https://github.com/marcelm/cutadapt/issues/128","id":81971640,"number":128,"title":"\"Reads written\" counts both trimmed and untrimmed reads","user":{"login":"marcelm","id":724864,"avatar_url":"https://avatars.githubusercontent.com/u/724864?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelm","html_url":"https://github.com/marcelm","followers_url":"https://api.github.com/users/marcelm/followers","following_url":"https://api.github.com/users/marcelm/following{/other_user}","gists_url":"https://api.github.com/users/marcelm/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelm/subscriptions","organizations_url":"https://api.github.com/users/marcelm/orgs","repos_url":"https://api.github.com/users/marcelm/repos","events_url":"https://api.github.com/users/marcelm/events{/privacy}","received_events_url":"https://api.github.com/users/marcelm/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-05-28T15:04:40Z","updated_at":"2015-09-14T09:58:59Z","closed_at":null,"body":"In the summary stats, the \"Reads written (passing filters)\" figure includes both trimmed and untrimmed reads. This can be confusing if trimmed and untrimmed reads are written to different output files since then the number is the sum of both. See also issue #126."},"comment":{"url":"https://api.github.com/repos/marcelm/cutadapt/issues/comments/140025261","html_url":"https://github.com/marcelm/cutadapt/issues/128#issuecomment-140025261","issue_url":"https://api.github.com/repos/marcelm/cutadapt/issues/128","id":140025261,"user":{"login":"marcelm","id":724864,"avatar_url":"https://avatars.githubusercontent.com/u/724864?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelm","html_url":"https://github.com/marcelm","followers_url":"https://api.github.com/users/marcelm/followers","following_url":"https://api.github.com/users/marcelm/following{/other_user}","gists_url":"https://api.github.com/users/marcelm/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelm/subscriptions","organizations_url":"https://api.github.com/users/marcelm/orgs","repos_url":"https://api.github.com/users/marcelm/repos","events_url":"https://api.github.com/users/marcelm/events{/privacy}","received_events_url":"https://api.github.com/users/marcelm/received_events","type":"User","site_admin":false},"created_at":"2015-09-14T09:58:59Z","updated_at":"2015-09-14T09:58:59Z","body":"I think that’s a bug: It seems that reads that should be discarded are actually written to the output file. The statistics is “correct” in the sense that it properly describes how many read pairs have been erroneously written to the output files. I’ll try to come up with a fix."}}