{"action":"created","issue":{"url":"https://api.github.com/repos/Ensembl/ensembl-io/issues/27","repository_url":"https://api.github.com/repos/Ensembl/ensembl-io","labels_url":"https://api.github.com/repos/Ensembl/ensembl-io/issues/27/labels{/name}","comments_url":"https://api.github.com/repos/Ensembl/ensembl-io/issues/27/comments","events_url":"https://api.github.com/repos/Ensembl/ensembl-io/issues/27/events","html_url":"https://github.com/Ensembl/ensembl-io/pull/27","id":131378485,"number":27,"title":"Attempting to fix the currently breaking test suite.","user":{"login":"andrewyatz","id":178457,"avatar_url":"https://avatars.githubusercontent.com/u/178457?v=3","gravatar_id":"","url":"https://api.github.com/users/andrewyatz","html_url":"https://github.com/andrewyatz","followers_url":"https://api.github.com/users/andrewyatz/followers","following_url":"https://api.github.com/users/andrewyatz/following{/other_user}","gists_url":"https://api.github.com/users/andrewyatz/gists{/gist_id}","starred_url":"https://api.github.com/users/andrewyatz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrewyatz/subscriptions","organizations_url":"https://api.github.com/users/andrewyatz/orgs","repos_url":"https://api.github.com/users/andrewyatz/repos","events_url":"https://api.github.com/users/andrewyatz/events{/privacy}","received_events_url":"https://api.github.com/users/andrewyatz/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-02-04T15:14:57Z","updated_at":"2016-02-04T15:16:33Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/Ensembl/ensembl-io/pulls/27","html_url":"https://github.com/Ensembl/ensembl-io/pull/27","diff_url":"https://github.com/Ensembl/ensembl-io/pull/27.diff","patch_url":"https://github.com/Ensembl/ensembl-io/pull/27.patch"},"body":"**THIS CANNOT BE MERGED IN YET. DO NOT MERGE**\r\n\r\nThis branch is a set of changes to master to make sure the test suite runs once again. Already there have been some hidden bugs (seek() in BigWig not `-1` from the given start position) and removal of scripts masquerading as test cases.\r\n\r\nThere are still some issues with the VEP output code. From what I have seen the input file lacks the following columns\r\n\r\n- [ ] consequence\r\n- [ ] impact\r\n- [ ] exon\r\n- [ ] intron\r\n- [ ] hgvsc\r\n- [ ] hgvsp\r\n\r\nAre these actually fields in the VEP output or do they come from the final attributes set? Either the input file needs changing or the `VEP_output.pm` parser needs changing."},"comment":{"url":"https://api.github.com/repos/Ensembl/ensembl-io/issues/comments/179894128","html_url":"https://github.com/Ensembl/ensembl-io/pull/27#issuecomment-179894128","issue_url":"https://api.github.com/repos/Ensembl/ensembl-io/issues/27","id":179894128,"user":{"login":"andrewyatz","id":178457,"avatar_url":"https://avatars.githubusercontent.com/u/178457?v=3","gravatar_id":"","url":"https://api.github.com/users/andrewyatz","html_url":"https://github.com/andrewyatz","followers_url":"https://api.github.com/users/andrewyatz/followers","following_url":"https://api.github.com/users/andrewyatz/following{/other_user}","gists_url":"https://api.github.com/users/andrewyatz/gists{/gist_id}","starred_url":"https://api.github.com/users/andrewyatz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrewyatz/subscriptions","organizations_url":"https://api.github.com/users/andrewyatz/orgs","repos_url":"https://api.github.com/users/andrewyatz/repos","events_url":"https://api.github.com/users/andrewyatz/events{/privacy}","received_events_url":"https://api.github.com/users/andrewyatz/received_events","type":"User","site_admin":false},"created_at":"2016-02-04T15:16:33Z","updated_at":"2016-02-04T15:16:33Z","body":"Leaving a note for @ens-ap5 and @ens-ds23. @ens-ap5 you should check about VEP output. @ens-ds23 I want to make sure there's nothing I've broken here for the web especially changing how seek() operates. Also can you tell me if the test cases for bigBed and bigWig are operating as you expect them to as a client of the code? Thanks "}}