{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/701","repository_url":"https://api.github.com/repos/broadinstitute/picard","labels_url":"https://api.github.com/repos/broadinstitute/picard/issues/701/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/701/comments","events_url":"https://api.github.com/repos/broadinstitute/picard/issues/701/events","html_url":"https://github.com/broadinstitute/picard/pull/701","id":194449688,"number":701,"title":"Small changes to how MBA works with bacterial contamination","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":8,"created_at":"2016-12-08T21:30:41Z","updated_at":"2016-12-09T20:05:03Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/701","html_url":"https://github.com/broadinstitute/picard/pull/701","diff_url":"https://github.com/broadinstitute/picard/pull/701.diff","patch_url":"https://github.com/broadinstitute/picard/pull/701.patch"},"body":"### Description\r\nMBA currently unmaps reads that are suspect of being Bacterial contamination. There are severl limitations in the implementation:\r\n1. The (old) mapping information is discarded when converted to CRAM format\r\n2. The FT: tag (into which a note is placed regarding the change made was confusing and not in the SAM spec\r\n3. The log files explode when there are many reads that look like bacterial contamination.\r\n\r\nThis PR solves each of these as follows:\r\n\r\n1. The old mapping is placed into a PA tag with encoding like the AS tag\r\n2. instead of FT it now uses the CO tag (COmment) with a `|` separator incase that there already was a comment\r\n3. limit number of warnings to 1000, with one extra warning at 1000 stateing that no more warnings to that effect will be posted.\r\n\r\n----\r\n\r\n### Checklist (never delete this)\r\n\r\nNever delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below.\r\n\r\n#### Content\r\n- [X] Added or modified tests to cover changes and any new functionality\r\n- [ ] Edited the README / documentation (if applicable)\r\n- [ ] All tests passing on Travis\r\n\r\n#### Review\r\n- [ ] Final thumbs-up from reviewer\r\n- [ ] Rebase, squash and reword as applicable\r\n\r\nFor more detailed guidelines, see https://github.com/broadinstitute/picard/wiki/Guidelines-for-pull-requests\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/comments/266109858","html_url":"https://github.com/broadinstitute/picard/pull/701#issuecomment-266109858","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/701","id":266109858,"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":"2016-12-09T20:05:03Z","updated_at":"2016-12-09T20:05:03Z","body":"\n[![Coverage Status](https://coveralls.io/builds/9213754/badge)](https://coveralls.io/builds/9213754)\n\nCoverage increased (+0.04%) to 71.112% when pulling **a87e520e3aa50b854fc92e1781d7cc60e6dd639c on yf_change_bacterialContamination_to_filter** into **5798733acc87f55eb25c02413827b22bd384f80c on master**.\n"}}
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