{"action":"created","issue":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1930","repository_url":"https://api.github.com/repos/galaxyproject/galaxy","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1930/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1930/comments","events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1930/events","html_url":"https://github.com/galaxyproject/galaxy/pull/1930","id":141062579,"number":1930,"title":"[16.01] Ensure chrom, start, end as bytestring in BamDataProvider","user":{"login":"mvdbeek","id":6804901,"avatar_url":"https://avatars.githubusercontent.com/u/6804901?v=3","gravatar_id":"","url":"https://api.github.com/users/mvdbeek","html_url":"https://github.com/mvdbeek","followers_url":"https://api.github.com/users/mvdbeek/followers","following_url":"https://api.github.com/users/mvdbeek/following{/other_user}","gists_url":"https://api.github.com/users/mvdbeek/gists{/gist_id}","starred_url":"https://api.github.com/users/mvdbeek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mvdbeek/subscriptions","organizations_url":"https://api.github.com/users/mvdbeek/orgs","repos_url":"https://api.github.com/users/mvdbeek/repos","events_url":"https://api.github.com/users/mvdbeek/events{/privacy}","received_events_url":"https://api.github.com/users/mvdbeek/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2016-03-15T18:35:25Z","updated_at":"2016-04-11T15:14:22Z","closed_at":"2016-03-15T20:16:22Z","pull_request":{"url":"https://api.github.com/repos/galaxyproject/galaxy/pulls/1930","html_url":"https://github.com/galaxyproject/galaxy/pull/1930","diff_url":"https://github.com/galaxyproject/galaxy/pull/1930.diff","patch_url":"https://github.com/galaxyproject/galaxy/pull/1930.patch"},"body":"This should fix an error report that just came in on the mailing list by Lubos Klucar\r\n\r\n```\r\ngalaxy.webapps.galaxy.api.datasets ERROR 2016-03-15 11:44:38,853 Error in dataset API at listing contents: Expected bytes, got unicode: Expected bytes, got unicode\r\nTraceback (most recent call last):\r\n  File \"/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py\", line 66, in show\r\n    rval = self._data( trans, dataset, **kwd )\r\n  File \"/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py\", line 235, in _data\r\n    ref_seq=region, mean_depth=mean_depth, **kwargs )\r\n  File \"/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py\", line 192, in get_data\r\n    iterator = self.get_iterator( data_file, chrom, start, end, **kwargs )\r\n  File \"/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py\", line 892, in get_iterator\r\n    data = data_file.fetch( start=start, end=end, reference=chrom )\r\n  File \"pysam/calignmentfile.pyx\", line 868, in pysam.calignmentfile.AlignmentFile.fetch (pysam/calignmentfile.c:10170)\r\n  File \"pysam/calignmentfile.pyx\", line 787, in pysam.calignmentfile.AlignmentFile.parse_region (pysam/calignmentfile.c:9605)\r\n  File \"pysam/calignmentfile.pyx\", line 1576, in pysam.calignmentfile.AlignmentFile.gettid (pysam/calignmentfile.c:16665)\r\n  File \"pysam/calignmentfile.pyx\", line 640, in pysam.calignmentfile.AlignmentFile.get_tid (pysam/calignmentfile.c:8208)\r\n  File \"pysam/cutils.pyx\", line 106, in pysam.cutils.force_bytes (pysam/cutils.c:2170)\r\nTypeError: Expected bytes, got unicode\r\n```\r\n\r\nPing @nsoranzo @dannon, this seems to be the same issue as in PR #1897 \r\nThough I'm very surprised that noone has reported an error before!"},"comment":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/comments/208396005","html_url":"https://github.com/galaxyproject/galaxy/pull/1930#issuecomment-208396005","issue_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/1930","id":208396005,"user":{"login":"galaxybot","id":14315658,"avatar_url":"https://avatars.githubusercontent.com/u/14315658?v=3","gravatar_id":"","url":"https://api.github.com/users/galaxybot","html_url":"https://github.com/galaxybot","followers_url":"https://api.github.com/users/galaxybot/followers","following_url":"https://api.github.com/users/galaxybot/following{/other_user}","gists_url":"https://api.github.com/users/galaxybot/gists{/gist_id}","starred_url":"https://api.github.com/users/galaxybot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/galaxybot/subscriptions","organizations_url":"https://api.github.com/users/galaxybot/orgs","repos_url":"https://api.github.com/users/galaxybot/repos","events_url":"https://api.github.com/users/galaxybot/events{/privacy}","received_events_url":"https://api.github.com/users/galaxybot/received_events","type":"User","site_admin":false},"created_at":"2016-04-11T15:14:22Z","updated_at":"2016-04-11T15:14:22Z","body":"This PR was merged without a milestone attached."}}