{"action":"opened","issue":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/674","repository_url":"https://api.github.com/repos/broadinstitute/viral-ngs","labels_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/674/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/674/comments","events_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/674/events","html_url":"https://github.com/broadinstitute/viral-ngs/issues/674","id":260280146,"number":674,"title":"tolerate bad line endings in samplesheets","user":{"login":"dpark01","id":8513746,"avatar_url":"https://avatars2.githubusercontent.com/u/8513746?v=4","gravatar_id":"","url":"https://api.github.com/users/dpark01","html_url":"https://github.com/dpark01","followers_url":"https://api.github.com/users/dpark01/followers","following_url":"https://api.github.com/users/dpark01/following{/other_user}","gists_url":"https://api.github.com/users/dpark01/gists{/gist_id}","starred_url":"https://api.github.com/users/dpark01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpark01/subscriptions","organizations_url":"https://api.github.com/users/dpark01/orgs","repos_url":"https://api.github.com/users/dpark01/repos","events_url":"https://api.github.com/users/dpark01/events{/privacy}","received_events_url":"https://api.github.com/users/dpark01/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-09-25T13:39:17Z","updated_at":"2017-09-25T13:39:17Z","closed_at":null,"author_association":"COLLABORATOR","body":"Although most of our csv-reading samplesheet code tolerates MS Excel-generated files (with Mac OS9 line endings), our txt-reading samplesheet code does not. In particular, `util.file.read_tabfile_dict` (and the related `read_tabfile`) are opening files as `'rt'` instead of `'rU'`. This is one of the dumber error modes that frequently happens that Redmond, WA imposes on us, but we must deal with."}}
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