{"action":"opened","issue":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/13","labels_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/13/comments","events_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/13/events","html_url":"https://github.com/COMBINE-lab/salmon/issues/13","id":108007727,"number":13,"title":"Check for non-random ordered reads and fail","user":{"login":"bwlang","id":61636,"avatar_url":"https://avatars.githubusercontent.com/u/61636?v=3","gravatar_id":"","url":"https://api.github.com/users/bwlang","html_url":"https://github.com/bwlang","followers_url":"https://api.github.com/users/bwlang/followers","following_url":"https://api.github.com/users/bwlang/following{/other_user}","gists_url":"https://api.github.com/users/bwlang/gists{/gist_id}","starred_url":"https://api.github.com/users/bwlang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bwlang/subscriptions","organizations_url":"https://api.github.com/users/bwlang/orgs","repos_url":"https://api.github.com/users/bwlang/repos","events_url":"https://api.github.com/users/bwlang/events{/privacy}","received_events_url":"https://api.github.com/users/bwlang/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-09-23T21:13:33Z","updated_at":"2015-09-23T21:13:33Z","closed_at":null,"body":"I think the requirement for random ordered reads is surprising for some... \r\nDocumentation is good, but given how consequential it is to run with ordered reads (see https://twitter.com/KeywanHP/status/646661366774923264), would it make sense to fail if the first 1000 reads are from the same chr and position increases monotonically?\r\nOr at minimum, fail if the BAM has a so:coordinate header.\r\n\r\n\r\n"}}