{"action":"closed","issue":{"url":"https://api.github.com/repos/samtools/samtools/issues/485","labels_url":"https://api.github.com/repos/samtools/samtools/issues/485/labels{/name}","comments_url":"https://api.github.com/repos/samtools/samtools/issues/485/comments","events_url":"https://api.github.com/repos/samtools/samtools/issues/485/events","html_url":"https://github.com/samtools/samtools/issues/485","id":116412427,"number":485,"title":"Argument for index file","user":{"login":"AlistairNWard","id":523111,"avatar_url":"https://avatars.githubusercontent.com/u/523111?v=3","gravatar_id":"","url":"https://api.github.com/users/AlistairNWard","html_url":"https://github.com/AlistairNWard","followers_url":"https://api.github.com/users/AlistairNWard/followers","following_url":"https://api.github.com/users/AlistairNWard/following{/other_user}","gists_url":"https://api.github.com/users/AlistairNWard/gists{/gist_id}","starred_url":"https://api.github.com/users/AlistairNWard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AlistairNWard/subscriptions","organizations_url":"https://api.github.com/users/AlistairNWard/orgs","repos_url":"https://api.github.com/users/AlistairNWard/repos","events_url":"https://api.github.com/users/AlistairNWard/events{/privacy}","received_events_url":"https://api.github.com/users/AlistairNWard/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-11-11T20:12:42Z","updated_at":"2015-11-11T20:34:01Z","closed_at":"2015-11-11T20:34:01Z","body":"Would it be possible to include a command line argument for the BAM index? Currently, assuming the index has FILE.bam.bai extension fails when tools, e.g. Picard have been used to generate an index of the form FILE.bai. If there is a command line argument, we can assume FILE.bam.bai in its absence, or use the value specified otherwise.\r\n\r\nThis is a significant overhead at the moment, so would really appreciate this simple fix."}}