{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/2350","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2350/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2350/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2350/events","html_url":"https://github.com/broadinstitute/gatk/pull/2350","id":201907124,"number":2350,"title":"Optimization of intervals on Spark","user":{"login":"tomwhite","id":85085,"avatar_url":"https://avatars0.githubusercontent.com/u/85085?v=3","gravatar_id":"","url":"https://api.github.com/users/tomwhite","html_url":"https://github.com/tomwhite","followers_url":"https://api.github.com/users/tomwhite/followers","following_url":"https://api.github.com/users/tomwhite/following{/other_user}","gists_url":"https://api.github.com/users/tomwhite/gists{/gist_id}","starred_url":"https://api.github.com/users/tomwhite/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tomwhite/subscriptions","organizations_url":"https://api.github.com/users/tomwhite/orgs","repos_url":"https://api.github.com/users/tomwhite/repos","events_url":"https://api.github.com/users/tomwhite/events{/privacy}","received_events_url":"https://api.github.com/users/tomwhite/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"droazen","id":798637,"avatar_url":"https://avatars3.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"assignees":[{"login":"droazen","id":798637,"avatar_url":"https://avatars3.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false}],"milestone":null,"comments":4,"created_at":"2017-01-19T16:24:00Z","updated_at":"2017-03-08T17:43:58Z","closed_at":"2017-03-08T17:43:12Z","pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/2350","html_url":"https://github.com/broadinstitute/gatk/pull/2350","diff_url":"https://github.com/broadinstitute/gatk/pull/2350.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/2350.patch"},"body":"Optimization of intervals on Spark, so that specifying intervals is faster than not using intervals.\r\n    \r\nSee https://github.com/HadoopGenomics/Hadoop-BAM/issues/91.\r\n    \r\n* With this change Hadoop-BAM no longer supports the\r\nKEEP_PAIRED_READS_TOGETHER_PROPERTY property, so this is now\r\nimplemented in BwaSparkEngine (which is the only place that uses it.)\r\n* Remove use of IntervalUtils.getAllIntervalsForReference in\r\nReadsSparkSource, since not specifying intervals now returns all\r\nreads.\r\n* Add coalesce(1) to ensure that example Spark walkers produce one\r\noutput file (some failed with this change).\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/285113045","html_url":"https://github.com/broadinstitute/gatk/pull/2350#issuecomment-285113045","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/2350","id":285113045,"user":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars0.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"created_at":"2017-03-08T17:43:58Z","updated_at":"2017-03-08T17:43:58Z","body":"yay!"}}
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