{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/776","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/776/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/776/comments","events_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/776/events","html_url":"https://github.com/broadinstitute/hellbender/issues/776","id":98778517,"number":776,"title":"Explain when there will be more than two reads with the same name in MarkDuplicates","user":{"login":"tovanadler","id":12535215,"avatar_url":"https://avatars.githubusercontent.com/u/12535215?v=3","gravatar_id":"","url":"https://api.github.com/users/tovanadler","html_url":"https://github.com/tovanadler","followers_url":"https://api.github.com/users/tovanadler/followers","following_url":"https://api.github.com/users/tovanadler/following{/other_user}","gists_url":"https://api.github.com/users/tovanadler/gists{/gist_id}","starred_url":"https://api.github.com/users/tovanadler/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tovanadler/subscriptions","organizations_url":"https://api.github.com/users/tovanadler/orgs","repos_url":"https://api.github.com/users/tovanadler/repos","events_url":"https://api.github.com/users/tovanadler/events{/privacy}","received_events_url":"https://api.github.com/users/tovanadler/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/DeveloperDoc","name":"DeveloperDoc","color":"5319e7"},{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/Help%20Wanted%20(Broad)","name":"Help Wanted (Broad)","color":"009800"},{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/broadinstitute/hellbender/milestones/5","html_url":"https://github.com/broadinstitute/hellbender/milestones/alpha","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/milestones/5/labels","id":1220227,"number":5,"title":"alpha","description":"","creator":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"open_issues":82,"closed_issues":19,"state":"open","created_at":"2015-07-22T13:37:37Z","updated_at":"2015-08-06T15:36:11Z","due_on":"2015-10-31T04:00:00Z","closed_at":null},"comments":2,"created_at":"2015-08-03T16:14:09Z","updated_at":"2015-08-07T03:29:03Z","closed_at":null,"body":"MarkDuplicatesDataflow has a function called labelPairedEndsWithAlignmentInfo that sorts the reads and then pairs them up. I am not sure why there would ever be more than two here, so if someone could add an explanation, that would be great."},"comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/comments/128578492","html_url":"https://github.com/broadinstitute/hellbender/issues/776#issuecomment-128578492","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/776","id":128578492,"user":{"login":"jean-philippe-martin","id":10458949,"avatar_url":"https://avatars.githubusercontent.com/u/10458949?v=3","gravatar_id":"","url":"https://api.github.com/users/jean-philippe-martin","html_url":"https://github.com/jean-philippe-martin","followers_url":"https://api.github.com/users/jean-philippe-martin/followers","following_url":"https://api.github.com/users/jean-philippe-martin/following{/other_user}","gists_url":"https://api.github.com/users/jean-philippe-martin/gists{/gist_id}","starred_url":"https://api.github.com/users/jean-philippe-martin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jean-philippe-martin/subscriptions","organizations_url":"https://api.github.com/users/jean-philippe-martin/orgs","repos_url":"https://api.github.com/users/jean-philippe-martin/repos","events_url":"https://api.github.com/users/jean-philippe-martin/events{/privacy}","received_events_url":"https://api.github.com/users/jean-philippe-martin/received_events","type":"User","site_admin":false},"created_at":"2015-08-07T03:29:03Z","updated_at":"2015-08-07T03:29:03Z","body":"I don't know the answer, but in the interest of moving forward, the function you mean is now called\r\n[keyPairedEndsWithAlignmentInfo](https://github.com/broadinstitute/hellbender/blob/master/src/main/java/org/broadinstitute/hellbender/tools/dataflow/transforms/markduplicates/MarkDuplicatesUtils.java#L110).\r\n\r\n"}}