{"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":3,"created_at":"2016-10-18T13:58:56Z","updated_at":"2016-10-19T14:32:14Z","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/254830816","html_url":"https://github.com/broadinstitute/picard/pull/676#issuecomment-254830816","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/676","id":254830816,"user":{"login":"coveralls","id":2354108,"avatar_url":"https://avatars.githubusercontent.com/u/2354108?v=3","gravatar_id":"","url":"https://api.github.com/users/coveralls","html_url":"https://github.com/coveralls","followers_url":"https://api.github.com/users/coveralls/followers","following_url":"https://api.github.com/users/coveralls/following{/other_user}","gists_url":"https://api.github.com/users/coveralls/gists{/gist_id}","starred_url":"https://api.github.com/users/coveralls/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/coveralls/subscriptions","organizations_url":"https://api.github.com/users/coveralls/orgs","repos_url":"https://api.github.com/users/coveralls/repos","events_url":"https://api.github.com/users/coveralls/events{/privacy}","received_events_url":"https://api.github.com/users/coveralls/received_events","type":"User","site_admin":false},"created_at":"2016-10-19T14:32:14Z","updated_at":"2016-10-19T14:32:14Z","body":"\n[![Coverage Status](https://coveralls.io/builds/8411078/badge)](https://coveralls.io/builds/8411078)\n\nCoverage increased (+0.005%) to 70.286% when pulling **b2b32770fbe3e9cb9ebfd2f16ca4cffb2d172f67 on yf_change_bacterialContamination_to_filter** into **4a55d813024cb9ab485e45f9575c60ea7e2fcf15 on master**.\n"}}
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