{"action":"created","issue":{"url":"https://api.github.com/repos/lomereiter/sambamba/issues/138","labels_url":"https://api.github.com/repos/lomereiter/sambamba/issues/138/labels{/name}","comments_url":"https://api.github.com/repos/lomereiter/sambamba/issues/138/comments","events_url":"https://api.github.com/repos/lomereiter/sambamba/issues/138/events","html_url":"https://github.com/lomereiter/sambamba/issues/138","id":70707648,"number":138,"title":"Sambamba index, incosistent command line usage and documentation","user":{"login":"rernst","id":2519331,"avatar_url":"https://avatars.githubusercontent.com/u/2519331?v=3","gravatar_id":"","url":"https://api.github.com/users/rernst","html_url":"https://github.com/rernst","followers_url":"https://api.github.com/users/rernst/followers","following_url":"https://api.github.com/users/rernst/following{/other_user}","gists_url":"https://api.github.com/users/rernst/gists{/gist_id}","starred_url":"https://api.github.com/users/rernst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rernst/subscriptions","organizations_url":"https://api.github.com/users/rernst/orgs","repos_url":"https://api.github.com/users/rernst/repos","events_url":"https://api.github.com/users/rernst/events{/privacy}","received_events_url":"https://api.github.com/users/rernst/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-04-24T14:42:08Z","updated_at":"2015-04-28T08:21:51Z","closed_at":null,"body":"The documentation (github.io) states that sambamba index can be used as follows: sambamba index <input.bam> <output.bai>. Where we the output.bai file is optional. This seems to be changed somewhere between 0.4.7 and 0.5.4, as currently it is not possible to to give an output.bai: \"sambamba-index <input.bam>\". \r\n\r\nIs this a bug or inconsistent documentation? I can't find the change in the release notes, I would expect it to be in there as this is changing the behaviour of sambamba index (our pipeline crashed). "},"comment":{"url":"https://api.github.com/repos/lomereiter/sambamba/issues/comments/96970812","html_url":"https://github.com/lomereiter/sambamba/issues/138#issuecomment-96970812","issue_url":"https://api.github.com/repos/lomereiter/sambamba/issues/138","id":96970812,"user":{"login":"rernst","id":2519331,"avatar_url":"https://avatars.githubusercontent.com/u/2519331?v=3","gravatar_id":"","url":"https://api.github.com/users/rernst","html_url":"https://github.com/rernst","followers_url":"https://api.github.com/users/rernst/followers","following_url":"https://api.github.com/users/rernst/following{/other_user}","gists_url":"https://api.github.com/users/rernst/gists{/gist_id}","starred_url":"https://api.github.com/users/rernst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rernst/subscriptions","organizations_url":"https://api.github.com/users/rernst/orgs","repos_url":"https://api.github.com/users/rernst/repos","events_url":"https://api.github.com/users/rernst/events{/privacy}","received_events_url":"https://api.github.com/users/rernst/received_events","type":"User","site_admin":false},"created_at":"2015-04-28T08:21:51Z","updated_at":"2015-04-28T08:21:51Z","body":"I agree with @pjotrp. I also asked Ies and he says there are indeed some tools that need a \"sample.bai\". For example, freebayes."}}