{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/278","repository_url":"https://api.github.com/repos/broadinstitute/gatk-protected","labels_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/278/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/278/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/278/events","html_url":"https://github.com/broadinstitute/gatk-protected/issues/278","id":125213091,"number":278,"title":"Do we still want these methods (e.g. betathats, tangentNormalization) attached to the PoN interface?","user":{"login":"LeeTL1220","id":2152339,"avatar_url":"https://avatars.githubusercontent.com/u/2152339?v=3","gravatar_id":"","url":"https://api.github.com/users/LeeTL1220","html_url":"https://github.com/LeeTL1220","followers_url":"https://api.github.com/users/LeeTL1220/followers","following_url":"https://api.github.com/users/LeeTL1220/following{/other_user}","gists_url":"https://api.github.com/users/LeeTL1220/gists{/gist_id}","starred_url":"https://api.github.com/users/LeeTL1220/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeeTL1220/subscriptions","organizations_url":"https://api.github.com/users/LeeTL1220/orgs","repos_url":"https://api.github.com/users/LeeTL1220/repos","events_url":"https://api.github.com/users/LeeTL1220/events{/privacy}","received_events_url":"https://api.github.com/users/LeeTL1220/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/labels/Copy%20Number%20tools","name":"Copy Number tools","color":"207de5"},{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/labels/question","name":"question","color":"cc317c"}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/milestones/8","html_url":"https://github.com/broadinstitute/gatk-protected/milestones/CNV%20Tools%20alpha-3%20release","labels_url":"https://api.github.com/repos/broadinstitute/gatk-protected/milestones/8/labels","id":1618160,"number":8,"title":"CNV Tools alpha-3 release","description":"#### CNV/ACNV improvements\r\n- Probabilistic-PCA coverage model\r\n- HMM segmentation\r\n- Germline CNV tool (probabilistic-PCA + HMM) with evaluation\r\n- Allelic panel of normals for ACNV\r\n\r\n#### WGS\r\n- ACNV for WGS\r\n- Evaluation of GATK CNV for WGS\r\n- Evaluation of GATK ACNV for WGS\r\n- GC correction and evaluation in WGS \r\n\r\n#### Other\r\n- WDL scripts for CNV/ACNV workflows (CreatePoN, Case)\r\n- Automated testing of workflows on Travis\r\n- Infrastructure for automated evaluations\r\n- Automated GATK CNV CRSP evaluation\r\n- Prototype tool for purity/ploidy inference","creator":{"login":"LeeTL1220","id":2152339,"avatar_url":"https://avatars.githubusercontent.com/u/2152339?v=3","gravatar_id":"","url":"https://api.github.com/users/LeeTL1220","html_url":"https://github.com/LeeTL1220","followers_url":"https://api.github.com/users/LeeTL1220/followers","following_url":"https://api.github.com/users/LeeTL1220/following{/other_user}","gists_url":"https://api.github.com/users/LeeTL1220/gists{/gist_id}","starred_url":"https://api.github.com/users/LeeTL1220/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeeTL1220/subscriptions","organizations_url":"https://api.github.com/users/LeeTL1220/orgs","repos_url":"https://api.github.com/users/LeeTL1220/repos","events_url":"https://api.github.com/users/LeeTL1220/events{/privacy}","received_events_url":"https://api.github.com/users/LeeTL1220/received_events","type":"User","site_admin":false},"open_issues":48,"closed_issues":46,"state":"open","created_at":"2016-03-02T15:52:34Z","updated_at":"2016-08-17T20:08:27Z","due_on":"2016-09-30T00:00:00Z","closed_at":null},"comments":3,"created_at":"2016-01-06T16:35:01Z","updated_at":"2016-08-17T20:08:27Z","closed_at":"2016-08-17T20:08:27Z","body":"In PoN.java...\r\n\r\nMost operations on a PoN are in the TangentNormalizer class.  The PoN class is mostly used to store data, not perform operations.\r\n\r\nShould we refactor these methods into TangentNormalizer?"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/comments/240531680","html_url":"https://github.com/broadinstitute/gatk-protected/issues/278#issuecomment-240531680","issue_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/278","id":240531680,"user":{"login":"samuelklee","id":11076296,"avatar_url":"https://avatars.githubusercontent.com/u/11076296?v=3","gravatar_id":"","url":"https://api.github.com/users/samuelklee","html_url":"https://github.com/samuelklee","followers_url":"https://api.github.com/users/samuelklee/followers","following_url":"https://api.github.com/users/samuelklee/following{/other_user}","gists_url":"https://api.github.com/users/samuelklee/gists{/gist_id}","starred_url":"https://api.github.com/users/samuelklee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/samuelklee/subscriptions","organizations_url":"https://api.github.com/users/samuelklee/orgs","repos_url":"https://api.github.com/users/samuelklee/repos","events_url":"https://api.github.com/users/samuelklee/events{/privacy}","received_events_url":"https://api.github.com/users/samuelklee/received_events","type":"User","site_admin":false},"created_at":"2016-08-17T20:08:27Z","updated_at":"2016-08-17T20:08:27Z","body":"Refactored in #618.  `CoveragePanelOfNormals` interface now only has a single `normalize` method."}}
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