{"action":"created","issue":{"url":"https://api.github.com/repos/pysam-developers/pysam/issues/254","repository_url":"https://api.github.com/repos/pysam-developers/pysam","labels_url":"https://api.github.com/repos/pysam-developers/pysam/issues/254/labels{/name}","comments_url":"https://api.github.com/repos/pysam-developers/pysam/issues/254/comments","events_url":"https://api.github.com/repos/pysam-developers/pysam/issues/254/events","html_url":"https://github.com/pysam-developers/pysam/issues/254","id":140565971,"number":254,"title":"Bedcov regression in pysam 0.9","user":{"login":"kyleabeauchamp","id":1900459,"avatar_url":"https://avatars.githubusercontent.com/u/1900459?v=3","gravatar_id":"","url":"https://api.github.com/users/kyleabeauchamp","html_url":"https://github.com/kyleabeauchamp","followers_url":"https://api.github.com/users/kyleabeauchamp/followers","following_url":"https://api.github.com/users/kyleabeauchamp/following{/other_user}","gists_url":"https://api.github.com/users/kyleabeauchamp/gists{/gist_id}","starred_url":"https://api.github.com/users/kyleabeauchamp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kyleabeauchamp/subscriptions","organizations_url":"https://api.github.com/users/kyleabeauchamp/orgs","repos_url":"https://api.github.com/users/kyleabeauchamp/repos","events_url":"https://api.github.com/users/kyleabeauchamp/events{/privacy}","received_events_url":"https://api.github.com/users/kyleabeauchamp/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-03-14T03:37:52Z","updated_at":"2016-03-14T18:17:49Z","closed_at":null,"body":"I've found that `pysam.bedcov` seems to have stopped working on my installation.  \r\n\r\n\r\n```\r\nimport pysam\r\n\r\nbam = \"my.bam\"\r\nbed = \"my.bed\"\r\n\r\nlines = pysam.bedcov(bed, bam)\r\n```\r\n\r\nOn pysam 0.8.4 I got a list of strings as output:\r\n\r\n```\r\n['chr1\\t ...]\r\n```\r\n\r\nBut on 0.9 I get\r\n\r\n```\r\nERROR - failed to write data to stream: <closed file '<stdout>', mode 'w' at 0x100292150>\r\n```\r\n\r\nI'm using bioconda installs of pysam on python 2.7.  I've seen the same behavior on OSX and linux.  "},"comment":{"url":"https://api.github.com/repos/pysam-developers/pysam/issues/comments/196452138","html_url":"https://github.com/pysam-developers/pysam/issues/254#issuecomment-196452138","issue_url":"https://api.github.com/repos/pysam-developers/pysam/issues/254","id":196452138,"user":{"login":"kyleabeauchamp","id":1900459,"avatar_url":"https://avatars.githubusercontent.com/u/1900459?v=3","gravatar_id":"","url":"https://api.github.com/users/kyleabeauchamp","html_url":"https://github.com/kyleabeauchamp","followers_url":"https://api.github.com/users/kyleabeauchamp/followers","following_url":"https://api.github.com/users/kyleabeauchamp/following{/other_user}","gists_url":"https://api.github.com/users/kyleabeauchamp/gists{/gist_id}","starred_url":"https://api.github.com/users/kyleabeauchamp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kyleabeauchamp/subscriptions","organizations_url":"https://api.github.com/users/kyleabeauchamp/orgs","repos_url":"https://api.github.com/users/kyleabeauchamp/repos","events_url":"https://api.github.com/users/kyleabeauchamp/events{/privacy}","received_events_url":"https://api.github.com/users/kyleabeauchamp/received_events","type":"User","site_admin":false},"created_at":"2016-03-14T18:17:49Z","updated_at":"2016-03-14T18:17:49Z","body":"Looks like this is a duplicate of #245"}}