{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/389","labels_url":"https://api.github.com/repos/broadinstitute/picard/issues/389/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/389/comments","events_url":"https://api.github.com/repos/broadinstitute/picard/issues/389/events","html_url":"https://github.com/broadinstitute/picard/pull/389","id":126209661,"number":389,"title":"DO NOT MERGE: First pass at adding optical duplicate flagging/removal into MarkDupes","user":{"login":"tfenne","id":1609210,"avatar_url":"https://avatars.githubusercontent.com/u/1609210?v=3","gravatar_id":"","url":"https://api.github.com/users/tfenne","html_url":"https://github.com/tfenne","followers_url":"https://api.github.com/users/tfenne/followers","following_url":"https://api.github.com/users/tfenne/following{/other_user}","gists_url":"https://api.github.com/users/tfenne/gists{/gist_id}","starred_url":"https://api.github.com/users/tfenne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tfenne/subscriptions","organizations_url":"https://api.github.com/users/tfenne/orgs","repos_url":"https://api.github.com/users/tfenne/repos","events_url":"https://api.github.com/users/tfenne/events{/privacy}","received_events_url":"https://api.github.com/users/tfenne/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-01-12T15:52:53Z","updated_at":"2016-01-21T21:23:40Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/389","html_url":"https://github.com/broadinstitute/picard/pull/389","diff_url":"https://github.com/broadinstitute/picard/pull/389.diff","patch_url":"https://github.com/broadinstitute/picard/pull/389.patch"},"body":"First pass at some changes to MarkDuplicates to allow optical (co-localized?) duplicates to be annotated in the output file and/or excluded from the output file.  So far support is only included in MarkDuplicates, though with a little help from @nh13 or @bradtaylor I'd be happy to extend support to MarkDuplicatesWithMateCigar also.\r\n\r\n@nh13, @yfarjoun : Could you take a first look at this please and let me know what you think of the direction I've taken?  I'm not ready (yet) for a detailed review, just looking to get some extra eyes on this before I sink more time into writing tests and shining it up.  Thanks!"},"comment":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/comments/173711870","html_url":"https://github.com/broadinstitute/picard/pull/389#issuecomment-173711870","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/389","id":173711870,"user":{"login":"sooheelee","id":11543866,"avatar_url":"https://avatars.githubusercontent.com/u/11543866?v=3","gravatar_id":"","url":"https://api.github.com/users/sooheelee","html_url":"https://github.com/sooheelee","followers_url":"https://api.github.com/users/sooheelee/followers","following_url":"https://api.github.com/users/sooheelee/following{/other_user}","gists_url":"https://api.github.com/users/sooheelee/gists{/gist_id}","starred_url":"https://api.github.com/users/sooheelee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sooheelee/subscriptions","organizations_url":"https://api.github.com/users/sooheelee/orgs","repos_url":"https://api.github.com/users/sooheelee/repos","events_url":"https://api.github.com/users/sooheelee/events{/privacy}","received_events_url":"https://api.github.com/users/sooheelee/received_events","type":"User","site_admin":false},"created_at":"2016-01-21T21:23:40Z","updated_at":"2016-01-21T21:23:40Z","body":"When are you planning to make this public? I've been working on an [updated  MarkDuplicates tutorial](http://gatkforums.broadinstitute.org/gatk/discussion/6747/how-to-flag-duplicates-with-markduplicates-or-markduplicateswithmatecigar#latest) that includes MarkDuplicatesWithMateCigar. "}}