{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/4769","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4769/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4769/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4769/events","html_url":"https://github.com/broadinstitute/gatk/pull/4769","id":323271376,"number":4769,"title":"Add BreakpointEvidence filter based on classifier","user":{"login":"TedBrookings","id":6463752,"avatar_url":"https://avatars2.githubusercontent.com/u/6463752?v=4","gravatar_id":"","url":"https://api.github.com/users/TedBrookings","html_url":"https://github.com/TedBrookings","followers_url":"https://api.github.com/users/TedBrookings/followers","following_url":"https://api.github.com/users/TedBrookings/following{/other_user}","gists_url":"https://api.github.com/users/TedBrookings/gists{/gist_id}","starred_url":"https://api.github.com/users/TedBrookings/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TedBrookings/subscriptions","organizations_url":"https://api.github.com/users/TedBrookings/orgs","repos_url":"https://api.github.com/users/TedBrookings/repos","events_url":"https://api.github.com/users/TedBrookings/events{/privacy}","received_events_url":"https://api.github.com/users/TedBrookings/received_events","type":"User","site_admin":false},"labels":[{"id":284415544,"url":"https://api.github.com/repos/broadinstitute/gatk/labels/SV","name":"SV","color":"207de5","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-05-15T15:33:02Z","updated_at":"2018-05-17T19:36:03Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/4769","html_url":"https://github.com/broadinstitute/gatk/pull/4769","diff_url":"https://github.com/broadinstitute/gatk/pull/4769.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/4769.patch"},"body":"Added XGBoostEvidenceFilter, an alternative BreakpointEvidence filter\r\nbased on XGBoost classifier.\r\n - Default is still BreakpointDensityFilter. Switch by passing\r\n   \"--sv-evidence-filter-type XGBOOST\" instead of \"DENSITY\".\r\n - Decisions based on evidence overlap or coherence are now scaled based\r\n   on coverage depth (in both filter types).\r\n - Multiple avenues for supplying saved classifier binary file,\r\n   including built-in resource, local file, and google cloud storage.\r\n - BreakpointEvidence updated to carry information necessary for\r\n   classifier. Unit tests were correspondingly updated.\r\n - Data from genome tracts used for some classifier features. From the\r\n   hg38 genome: gaps, centromeres, and umap s100.\r\n\r\nAdditional changes to convenience scripts\r\n - Updated sanity_checks.sh to return error signal when exiting\r\n - Bugfixes to manage_sv_pipeline.sh for linux compatibility\r\n - Update run_whole_pipeline.sh to detect preemptible workers and\r\n   thus set NUM_EXECUTORS correctly"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/389983715","html_url":"https://github.com/broadinstitute/gatk/pull/4769#issuecomment-389983715","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4769","id":389983715,"user":{"login":"davidbenjamin","id":8438890,"avatar_url":"https://avatars3.githubusercontent.com/u/8438890?v=4","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false},"created_at":"2018-05-17T19:36:03Z","updated_at":"2018-05-17T19:36:03Z","author_association":"CONTRIBUTOR","body":"And also, I agree that if you're working with an API like Spark that is based on iterators then you shouldn't transform them into Streams or a Collections.  Likewise if a problem is inherently online."}}
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