{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/676","repository_url":"https://api.github.com/repos/broadinstitute/picard","labels_url":"https://api.github.com/repos/broadinstitute/picard/issues/676/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/676/comments","events_url":"https://api.github.com/repos/broadinstitute/picard/issues/676/events","html_url":"https://github.com/broadinstitute/picard/pull/676","id":183694399,"number":676,"title":"Yf change bacterial contamination to filter","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},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2016-10-18T13:58:56Z","updated_at":"2016-10-19T23:51:24Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/676","html_url":"https://github.com/broadinstitute/picard/pull/676","diff_url":"https://github.com/broadinstitute/picard/pull/676.diff","patch_url":"https://github.com/broadinstitute/picard/pull/676.patch"},"body":"This PR changes the bahavior of MergeBamAlignment when encountering a read that looks like bacterial contamination (soft-clipped on both sides, and few unclipped bases left)\r\n\r\n- previous behavior: unmap read (and mate) and reset position\r\n- new behavior: filter (0x200 flag) read and mate, and leave mapping and other tags alone."},"comment":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/comments/254973130","html_url":"https://github.com/broadinstitute/picard/pull/676#issuecomment-254973130","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/676","id":254973130,"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":"2016-10-19T23:51:24Z","updated_at":"2016-10-19T23:51:24Z","body":"The revert-sam problem is indeed compelling....\n\nthe problem I'm faced with is the loss of the original data. Perhaps\nthere's a solution that will allow us to save the mapping data...\n\n\nOn Wed, Oct 19, 2016 at 3:59 PM, Tim Fennell <notifications@github.com>\nwrote:\n\n> I think the real downside of 0x200 (non-PF) is that unless any/all tools\n> that rely on that flag are updated to also look at the FT tag, things are\n> going to get lost. Imagine someone hands you a BAM that has these reads\n> with 0x200 set, and you decide you want to re-map the reads, so you\n> remove all the mapping information and excess tags, and start over. But if\n> you weren't careful then all these reads will still be set as non-PF and\n> might get skipped over.\n>\n> I think the previous method of making the read unmapped is more in line\n> with reality - you're saying you don't trust these very short/poor quality\n> mappings, so you want to ignore them.\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/broadinstitute/picard/pull/676#issuecomment-254923570>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/ACnk0vWRwBXfzrOqSedNL75bcv05Dwtxks5q1na8gaJpZM4KZ0t4>\n> .\n>\n"}}
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