{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/365","labels_url":"https://api.github.com/repos/broadinstitute/picard/issues/365/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/365/comments","events_url":"https://api.github.com/repos/broadinstitute/picard/issues/365/events","html_url":"https://github.com/broadinstitute/picard/pull/365","id":123521057,"number":365,"title":"Add capabilities to output both usable and raw metrics.","user":{"login":"eitanbanks","id":2751498,"avatar_url":"https://avatars.githubusercontent.com/u/2751498?v=3","gravatar_id":"","url":"https://api.github.com/users/eitanbanks","html_url":"https://github.com/eitanbanks","followers_url":"https://api.github.com/users/eitanbanks/followers","following_url":"https://api.github.com/users/eitanbanks/following{/other_user}","gists_url":"https://api.github.com/users/eitanbanks/gists{/gist_id}","starred_url":"https://api.github.com/users/eitanbanks/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eitanbanks/subscriptions","organizations_url":"https://api.github.com/users/eitanbanks/orgs","repos_url":"https://api.github.com/users/eitanbanks/repos","events_url":"https://api.github.com/users/eitanbanks/events{/privacy}","received_events_url":"https://api.github.com/users/eitanbanks/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-12-22T17:14:09Z","updated_at":"2015-12-22T23:03:16Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/365","html_url":"https://github.com/broadinstitute/picard/pull/365","diff_url":"https://github.com/broadinstitute/picard/pull/365.diff","patch_url":"https://github.com/broadinstitute/picard/pull/365.patch"},"body":"DO NOT MERGE.\r\n\r\nI'm still working on updating the tests.  But I wanted to get a quick code review from Yossi, Kathleen, and Jose given the time constraints.\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/comments/166757928","html_url":"https://github.com/broadinstitute/picard/pull/365#issuecomment-166757928","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/365","id":166757928,"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},"created_at":"2015-12-22T23:03:16Z","updated_at":"2015-12-22T23:03:16Z","body":"I want to document here that the \"raw\" metrics are defined according to Illumina's whitepaper: http://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/hiseq-x-30x-coverage-technical-note-770-2014-042.pdf, and while I think that it is not a good metric to be using since it counts unusable bases towards coverage, as long as some people use it, we think it best to avoid wrong calculations like the formula at the bottom of the cited white-paper.\r\n"}}