{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1434","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1434/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1434/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1434/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1434","id":160204196,"number":1434,"title":"Minor bug fix for simple_sv_annotation.py","user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2016-06-14T15:00:12Z","updated_at":"2016-07-01T14:47:45Z","closed_at":"2016-06-15T09:08:00Z","body":"AZ kindly contributed the simple_sv_annotation script, which is hosted by bioconda and used in bcbio. I have a minor bugfix for this module; however, it seems to be vanished from the AZ github repository at the moment. The bug fix is very simple; in line `218` of that file, it says:\r\n\r\n```python\r\n        exons.append(int(ann_a[8].split('/')[0]))\r\n```\r\n\r\nSometimes, the extracted values can be `''` (an empty string), in which case the cast to integer fails. The fix is to catch the error and pass on it:\r\n\r\n```python\r\n        try:\r\n            exons.append(int(ann_a[8].split('/')[0]))\r\n        except ValueError:\r\n            pass\r\n```\r\n@miika, perhaps you could comment on the script being lost from your repo, and could fix the bug in the bioconda version? Thanks a bunch."},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/229966370","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1434#issuecomment-229966370","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1434","id":229966370,"user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"created_at":"2016-07-01T14:47:45Z","updated_at":"2016-07-01T14:47:45Z","body":"Great, thanks for the update."}}
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