{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/44239017","id":44239017,"diff_hunk":"@@ -0,0 +1,9 @@\n+package picard.filter;","path":"src/java/picard/filter/CountingPairedFilter.java","position":1,"original_position":1,"commit_id":"e9862a032cc549e97e8b69c041bb76d8fbf77415","original_commit_id":"e9862a032cc549e97e8b69c041bb76d8fbf77415","user":{"login":"yfarjoun","id":2745554,"avatar_url":"https://avatars.githubusercontent.com/u/2745554?v=3","gravatar_id":"","url":"https://api.github.com/users/yfarjoun","html_url":"https://github.com/yfarjoun","followers_url":"https://api.github.com/users/yfarjoun/followers","following_url":"https://api.github.com/users/yfarjoun/following{/other_user}","gists_url":"https://api.github.com/users/yfarjoun/gists{/gist_id}","starred_url":"https://api.github.com/users/yfarjoun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yfarjoun/subscriptions","organizations_url":"https://api.github.com/users/yfarjoun/orgs","repos_url":"https://api.github.com/users/yfarjoun/repos","events_url":"https://api.github.com/users/yfarjoun/events{/privacy}","received_events_url":"https://api.github.com/users/yfarjoun/received_events","type":"User","site_admin":false},"body":"license","created_at":"2015-11-09T03:34:06Z","updated_at":"2015-11-09T03:34:06Z","html_url":"https://github.com/broadinstitute/picard/pull/332#discussion_r44239017","pull_request_url":"https://api.github.com/repos/broadinstitute/picard/pulls/332","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/44239017"},"html":{"href":"https://github.com/broadinstitute/picard/pull/332#discussion_r44239017"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/332"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/332","id":50022214,"html_url":"https://github.com/broadinstitute/picard/pull/332","diff_url":"https://github.com/broadinstitute/picard/pull/332.diff","patch_url":"https://github.com/broadinstitute/picard/pull/332.patch","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/332","number":332,"state":"open","locked":false,"title":"Modernizing Targeted Metrics Calculations","user":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"body":"@ktibbett @tfenne @yfarjoun there are a lot of updates to how we calculate targeted metrics, so likely a discussion is needed for this pull request.\r\n\r\nSome of the things to notice are:\r\n* now count bases in supplemental reads.\r\n* relax the minimum coverage all the way to zero for some of the metric values; previously the minimum coverage was two. @tfenne for a historical explanation.\r\n* deprecate ```CalculateHsMetrics``` in favor of ```CollectHsMetrics```, since this has always annoyed me.\r\n* added some new metrics.  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