{"action":"created","comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments/129497806","pull_request_review_id":52275861,"id":129497806,"diff_hunk":"@@ -275,4 +279,29 @@ public static String loadGenePanelInformation(File file) throws Exception {\n         properties.load(new FileInputStream(file));\n         return properties.getProperty(\"gene_panel\");\n     }\n+\n+\t/**\n+\t * Gets the information of \"variant_classification_filter\" in the file, if it exists. Otherwise, it\n+\t * returns null. \"variant_classification_filter\" can be used in the mutation meta file to specify\n+\t * which types of mutations want to be filtered.\n+\t * \n+\t * @param file\n+\t * @return a string with the types of mutations that should be filtered, comma-separated.\n+\t * @throws Exception\n+\t */\n+\tpublic static Set<String> getVariantClassificationFilter(File file) throws Exception {\n+\t    Properties properties = new TrimmedProperties();\n+\t    properties.load(new FileInputStream(file));\n+\t    String variantClassificationFilter = properties.getProperty(\"variant_classification_filter\");\n+\t    if (variantClassificationFilter != null) {\n+\t\t    Set<String> filteredMutations = new HashSet<String>();\n+\t\t    for (String mutation : (Arrays.asList(variantClassificationFilter.split(\",\")))) {\n+\t\t            mutation = mutation.trim();\n+\t\t            filteredMutations.add(mutation);\n+\t\t        }\n+\t\t    return filteredMutations;\n+\t    } else {\n+\t    \t\treturn null;","path":"core/src/main/java/org/mskcc/cbio/portal/util/GeneticProfileReader.java","position":null,"original_position":39,"commit_id":"8e395cdabc5579d6a84e87cc6012f2f2d2f20c52","original_commit_id":"f2fc74addbfbb3e95e4019726ca9e8a4971212bb","user":{"login":"oplantalech","id":20278013,"avatar_url":"https://avatars3.githubusercontent.com/u/20278013?v=4","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},"body":"Thanks for noticing! I've fixed it.","created_at":"2017-07-26T07:25:04Z","updated_at":"2017-07-26T07:25:04Z","html_url":"https://github.com/cBioPortal/cbioportal/pull/2670#discussion_r129497806","pull_request_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/2670","_links":{"self":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments/129497806"},"html":{"href":"https://github.com/cBioPortal/cbioportal/pull/2670#discussion_r129497806"},"pull_request":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/2670"}}},"pull_request":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/2670","id":127887274,"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","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/2670","number":2670,"state":"open","locked":false,"title":"Make filtering on mutation types configurable","user":{"login":"oplantalech","id":20278013,"avatar_url":"https://avatars3.githubusercontent.com/u/20278013?v=4","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},"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).\r\n\r\n[More information about this 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