{"action":"created","issue":{"url":"https://api.github.com/repos/pcingola/SnpEff/issues/74","labels_url":"https://api.github.com/repos/pcingola/SnpEff/issues/74/labels{/name}","comments_url":"https://api.github.com/repos/pcingola/SnpEff/issues/74/comments","events_url":"https://api.github.com/repos/pcingola/SnpEff/issues/74/events","html_url":"https://github.com/pcingola/SnpEff/issues/74","id":57807538,"number":74,"title":"Improve snpeff.config search","user":{"login":"pcingola","id":1334427,"avatar_url":"https://avatars.githubusercontent.com/u/1334427?v=3","gravatar_id":"","url":"https://api.github.com/users/pcingola","html_url":"https://github.com/pcingola","followers_url":"https://api.github.com/users/pcingola/followers","following_url":"https://api.github.com/users/pcingola/following{/other_user}","gists_url":"https://api.github.com/users/pcingola/gists{/gist_id}","starred_url":"https://api.github.com/users/pcingola/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pcingola/subscriptions","organizations_url":"https://api.github.com/users/pcingola/orgs","repos_url":"https://api.github.com/users/pcingola/repos","events_url":"https://api.github.com/users/pcingola/events{/privacy}","received_events_url":"https://api.github.com/users/pcingola/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/pcingola/SnpEff/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-02-16T14:02:14Z","updated_at":"2015-08-03T20:16:09Z","closed_at":"2015-08-03T20:16:09Z","body":"From a user:\r\n   The necessity to use the \"-c\" commandline switch to point to a config file is awkward. Why couldn't it look into $SNPEFF_CONFIG variable first, then fallback to /etc/snpEff.config and finally look in current working directory for the config file? One wouldn't need to use the \"-c\" switch almost at all. ;-)\r\n\r\n----------------------\r\nSo the search path would be:\r\n   i) Command line option \"-c\"\r\n   ii) Current dir\r\n   iii) JAR file's dir\r\n   iv) /etc/snpEff.config\r\n\r\nNote: Make sure to show search path in error message.\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/pcingola/SnpEff/issues/comments/127394929","html_url":"https://github.com/pcingola/SnpEff/issues/74#issuecomment-127394929","issue_url":"https://api.github.com/repos/pcingola/SnpEff/issues/74","id":127394929,"user":{"login":"pcingola","id":1334427,"avatar_url":"https://avatars.githubusercontent.com/u/1334427?v=3","gravatar_id":"","url":"https://api.github.com/users/pcingola","html_url":"https://github.com/pcingola","followers_url":"https://api.github.com/users/pcingola/followers","following_url":"https://api.github.com/users/pcingola/following{/other_user}","gists_url":"https://api.github.com/users/pcingola/gists{/gist_id}","starred_url":"https://api.github.com/users/pcingola/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pcingola/subscriptions","organizations_url":"https://api.github.com/users/pcingola/orgs","repos_url":"https://api.github.com/users/pcingola/repos","events_url":"https://api.github.com/users/pcingola/events{/privacy}","received_events_url":"https://api.github.com/users/pcingola/received_events","type":"User","site_admin":false},"created_at":"2015-08-03T20:16:09Z","updated_at":"2015-08-03T20:16:09Z","body":"Done."}}