{"action":"closed","issue":{"url":"https://api.github.com/repos/Cibiv/NextGenMap/issues/9","labels_url":"https://api.github.com/repos/Cibiv/NextGenMap/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/Cibiv/NextGenMap/issues/9/comments","events_url":"https://api.github.com/repos/Cibiv/NextGenMap/issues/9/events","html_url":"https://github.com/Cibiv/NextGenMap/issues/9","id":118648093,"number":9,"title":"0.4.13 on OSX","user":{"login":"breichholf","id":7795249,"avatar_url":"https://avatars.githubusercontent.com/u/7795249?v=3","gravatar_id":"","url":"https://api.github.com/users/breichholf","html_url":"https://github.com/breichholf","followers_url":"https://api.github.com/users/breichholf/followers","following_url":"https://api.github.com/users/breichholf/following{/other_user}","gists_url":"https://api.github.com/users/breichholf/gists{/gist_id}","starred_url":"https://api.github.com/users/breichholf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/breichholf/subscriptions","organizations_url":"https://api.github.com/users/breichholf/orgs","repos_url":"https://api.github.com/users/breichholf/repos","events_url":"https://api.github.com/users/breichholf/events{/privacy}","received_events_url":"https://api.github.com/users/breichholf/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-11-24T16:30:14Z","updated_at":"2015-12-10T15:12:04Z","closed_at":"2015-12-10T15:12:04Z","body":"Compiled with XCode 7.1 (AppleClang 7.0.0.7000176) which initially works fine. There are some minor compiler warnings in bamtools and seqan, but especially the former should be fixed with v2.4, according to their repo. In fact, I just tried it and bamtools-v2.4.0 does fix compiler warnings and compiles fine.\r\n\r\nRunning ngm then, however it crashes fairly early on:\r\nWhen using the `--output` parameter it crashes with the message:\r\n```\r\n[NGM] Opening for output (SAM): �]�\r\n[FILTER] Unable to open output file �]�\r\nThis error is fatal. Quitting...\r\n```\r\nWhen redirecting to stdout it crashes later on, as it thinks there are 0 reads in the input file.\r\nI think the error arises somewhere entirely different: `Config.GetString` or `InternalGet` seems to be the culprit. When debugging I do get proper return value, but couldn't track it down what the problem then seems to be. I did change the input and output names in the command line, but that only made it worse:\r\n```\r\n[MAIN] Query file (�_�) does not exist.\r\n```\r\nMaybe a problem with iostream/sstream?"}}