{"action":"created","issue":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/17","labels_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/17/comments","events_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/17/events","html_url":"https://github.com/cBioPortal/cbioportal/issues/17","id":75746164,"number":17,"title":"Mutation file format docs do not mention correct column for Amino_Acid_Change","user":{"login":"ecerami","id":1009066,"avatar_url":"https://avatars.githubusercontent.com/u/1009066?v=3","gravatar_id":"","url":"https://api.github.com/users/ecerami","html_url":"https://github.com/ecerami","followers_url":"https://api.github.com/users/ecerami/followers","following_url":"https://api.github.com/users/ecerami/following{/other_user}","gists_url":"https://api.github.com/users/ecerami/gists{/gist_id}","starred_url":"https://api.github.com/users/ecerami/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ecerami/subscriptions","organizations_url":"https://api.github.com/users/ecerami/orgs","repos_url":"https://api.github.com/users/ecerami/repos","events_url":"https://api.github.com/users/ecerami/events{/privacy}","received_events_url":"https://api.github.com/users/ecerami/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"ecerami","id":1009066,"avatar_url":"https://avatars.githubusercontent.com/u/1009066?v=3","gravatar_id":"","url":"https://api.github.com/users/ecerami","html_url":"https://github.com/ecerami","followers_url":"https://api.github.com/users/ecerami/followers","following_url":"https://api.github.com/users/ecerami/following{/other_user}","gists_url":"https://api.github.com/users/ecerami/gists{/gist_id}","starred_url":"https://api.github.com/users/ecerami/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ecerami/subscriptions","organizations_url":"https://api.github.com/users/ecerami/orgs","repos_url":"https://api.github.com/users/ecerami/repos","events_url":"https://api.github.com/users/ecerami/events{/privacy}","received_events_url":"https://api.github.com/users/ecerami/received_events","type":"User","site_admin":false},"milestone":null,"comments":9,"created_at":"2015-05-12T21:30:10Z","updated_at":"2015-05-14T18:54:44Z","closed_at":null,"body":"In this wiki document:\r\n\r\nhttps://github.com/cBioPortal/cbioportal/wiki/File-Formats#mutation-data\r\n\r\nwe do not specify the column name for \"Amino_Acid_Change\".  Assigning to self."},"comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/comments/102134528","html_url":"https://github.com/cBioPortal/cbioportal/issues/17#issuecomment-102134528","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/17","id":102134528,"user":{"login":"ecerami","id":1009066,"avatar_url":"https://avatars.githubusercontent.com/u/1009066?v=3","gravatar_id":"","url":"https://api.github.com/users/ecerami","html_url":"https://github.com/ecerami","followers_url":"https://api.github.com/users/ecerami/followers","following_url":"https://api.github.com/users/ecerami/following{/other_user}","gists_url":"https://api.github.com/users/ecerami/gists{/gist_id}","starred_url":"https://api.github.com/users/ecerami/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ecerami/subscriptions","organizations_url":"https://api.github.com/users/ecerami/orgs","repos_url":"https://api.github.com/users/ecerami/repos","events_url":"https://api.github.com/users/ecerami/events{/privacy}","received_events_url":"https://api.github.com/users/ecerami/received_events","type":"User","site_admin":false},"created_at":"2015-05-14T18:54:44Z","updated_at":"2015-05-14T18:54:44Z","body":"Ah, that's true.  AMINO_ACID_CHANGE is in the code.  But, if it's specified, it is stored in a separate field called aminoAcidChange, and only proteinChange is actually stored in the database.\r\n\r\nI am looking at this:  https://github.com/cBioPortal/cbioportal/blob/master/core/src/main/java/org/mskcc/cbio/maf/MafUtil.java\r\n\r\n    record.setProteinChange(TabDelimitedFileUtil.getPartString(getColumnIndex(PROTEIN_CHANGE), parts));\r\n\r\nand \r\n\r\n    public static final String PROTEIN_CHANGE = \"HGVSp_Short\";\r\n\r\nAnd in ExtendedMutationUtil:\r\n\r\n\t\tString proteinChange = record.getProteinChange();\r\n\r\n\t\t// if protein change is not valid, then use the string \"MUTATED\"\r\n\t\tif (!isValidProteinChange(proteinChange))\r\n\t\t{\r\n\t\t\tproteinChange = \"MUTATED\";\r\n\t\t}\r\n"}}