{"action":"created","issue":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/2670","repository_url":"https://api.github.com/repos/cBioPortal/cbioportal","labels_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/2670/labels{/name}","comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/2670/comments","events_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/2670/events","html_url":"https://github.com/cBioPortal/cbioportal/pull/2670","id":239115929,"number":2670,"title":"Make filtering on mutation types configurable","user":{"login":"oplantalech","id":20278013,"avatar_url":"https://avatars0.githubusercontent.com/u/20278013?v=3","gravatar_id":"","url":"https://api.github.com/users/oplantalech","html_url":"https://github.com/oplantalech","followers_url":"https://api.github.com/users/oplantalech/followers","following_url":"https://api.github.com/users/oplantalech/following{/other_user}","gists_url":"https://api.github.com/users/oplantalech/gists{/gist_id}","starred_url":"https://api.github.com/users/oplantalech/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/oplantalech/subscriptions","organizations_url":"https://api.github.com/users/oplantalech/orgs","repos_url":"https://api.github.com/users/oplantalech/repos","events_url":"https://api.github.com/users/oplantalech/events{/privacy}","received_events_url":"https://api.github.com/users/oplantalech/received_events","type":"User","site_admin":false},"labels":[{"id":284500045,"url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/feature","name":"feature","color":"009800","default":false},{"id":320679483,"url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/hyve","name":"hyve","color":"a0db8e","default":false},{"id":288494812,"url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/ready%20to%20review","name":"ready to review","color":"00bb00","default":false}],"state":"open","locked":false,"assignee":{"login":"pieterlukasse","id":2900303,"avatar_url":"https://avatars2.githubusercontent.com/u/2900303?v=3","gravatar_id":"","url":"https://api.github.com/users/pieterlukasse","html_url":"https://github.com/pieterlukasse","followers_url":"https://api.github.com/users/pieterlukasse/followers","following_url":"https://api.github.com/users/pieterlukasse/following{/other_user}","gists_url":"https://api.github.com/users/pieterlukasse/gists{/gist_id}","starred_url":"https://api.github.com/users/pieterlukasse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pieterlukasse/subscriptions","organizations_url":"https://api.github.com/users/pieterlukasse/orgs","repos_url":"https://api.github.com/users/pieterlukasse/repos","events_url":"https://api.github.com/users/pieterlukasse/events{/privacy}","received_events_url":"https://api.github.com/users/pieterlukasse/received_events","type":"User","site_admin":false},"assignees":[{"login":"pieterlukasse","id":2900303,"avatar_url":"https://avatars2.githubusercontent.com/u/2900303?v=3","gravatar_id":"","url":"https://api.github.com/users/pieterlukasse","html_url":"https://github.com/pieterlukasse","followers_url":"https://api.github.com/users/pieterlukasse/followers","following_url":"https://api.github.com/users/pieterlukasse/following{/other_user}","gists_url":"https://api.github.com/users/pieterlukasse/gists{/gist_id}","starred_url":"https://api.github.com/users/pieterlukasse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pieterlukasse/subscriptions","organizations_url":"https://api.github.com/users/pieterlukasse/orgs","repos_url":"https://api.github.com/users/pieterlukasse/repos","events_url":"https://api.github.com/users/pieterlukasse/events{/privacy}","received_events_url":"https://api.github.com/users/pieterlukasse/received_events","type":"User","site_admin":false}],"milestone":null,"comments":3,"created_at":"2017-06-28T10:11:09Z","updated_at":"2017-07-07T10:29:33Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/2670","html_url":"https://github.com/cBioPortal/cbioportal/pull/2670","diff_url":"https://github.com/cBioPortal/cbioportal/pull/2670.diff","patch_url":"https://github.com/cBioPortal/cbioportal/pull/2670.patch"},"body":"# What? Why?\r\nCurrently, cBioPortal filters out the following mutation types: `Silent`, `Intron`, `IGR`, `3'UTR`, `5'UTR`, `3'Flank` and `5'Flank`, except the promoter mutations for the TERT gene. We want to make this filtering by mutation type configurable by the user that loads studies in cBioPortal.\r\n\r\nChanges proposed in this pull request:\r\n- Add an optional field in the mutation meta file that specifies the mutation types that want to be filtered out. If the field is left empty, no mutation types are filtered. If the field is not written in the meta file, the default filtering done by cBioPortal is applied.\r\n\r\nThe parameter is called `variant_classification_filter`. The mutation types need to be written separated by a comma and following the [MAF nomenclature for Variant Classification](https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification)."},"comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/comments/313646453","html_url":"https://github.com/cBioPortal/cbioportal/pull/2670#issuecomment-313646453","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/2670","id":313646453,"user":{"login":"pieterlukasse","id":2900303,"avatar_url":"https://avatars2.githubusercontent.com/u/2900303?v=3","gravatar_id":"","url":"https://api.github.com/users/pieterlukasse","html_url":"https://github.com/pieterlukasse","followers_url":"https://api.github.com/users/pieterlukasse/followers","following_url":"https://api.github.com/users/pieterlukasse/following{/other_user}","gists_url":"https://api.github.com/users/pieterlukasse/gists{/gist_id}","starred_url":"https://api.github.com/users/pieterlukasse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pieterlukasse/subscriptions","organizations_url":"https://api.github.com/users/pieterlukasse/orgs","repos_url":"https://api.github.com/users/pieterlukasse/repos","events_url":"https://api.github.com/users/pieterlukasse/events{/privacy}","received_events_url":"https://api.github.com/users/pieterlukasse/received_events","type":"User","site_admin":false},"created_at":"2017-07-07T10:29:33Z","updated_at":"2017-07-07T10:29:33Z","body":"Nice, I like the new filtering table better."}}
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