{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1015","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1015/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1015/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1015/events","html_url":"https://github.com/broadinstitute/gatk/issues/1015","id":112175376,"number":1015,"title":"Make writing a single bam file in spark faster","user":{"login":"droazen","id":798637,"avatar_url":"https://avatars.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},"labels":[{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/Engine","name":"Engine","color":"5319e7"},{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/PRIORITY_HIGH","name":"PRIORITY_HIGH","color":"e11d21"},{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/profiling","name":"profiling","color":"bfd4f2"},{"url":"https://api.github.com/repos/broadinstitute/gatk/labels/Spark","name":"Spark","color":"FFD700"}],"state":"open","locked":false,"assignee":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/broadinstitute/gatk/milestones/5","html_url":"https://github.com/broadinstitute/gatk/milestones/alpha","labels_url":"https://api.github.com/repos/broadinstitute/gatk/milestones/5/labels","id":1220227,"number":5,"title":"alpha","description":"","creator":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"open_issues":31,"closed_issues":155,"state":"open","created_at":"2015-07-22T13:37:37Z","updated_at":"2015-11-23T18:40:05Z","due_on":"2015-12-04T05:00:00Z","closed_at":null},"comments":22,"created_at":"2015-10-19T15:57:40Z","updated_at":"2015-11-24T18:31:38Z","closed_at":null,"body":"`ReadsSparkSink.writeReadsSingle()` is unusably slow (even for small ouputs like a 200MB bam). We suspect this is due to its approach of calling `coalesce(1)`:\r\n\r\n        final JavaPairRDD<GATKRead, SAMRecordWritable> out =\r\n                rddSamRecordWriteable.sortByKey(new ReadCoordinateComparator(header)).coalesce(1);\r\n\r\nWe need to make it much faster in order to be able to use it in practice."},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/159364419","html_url":"https://github.com/broadinstitute/gatk/issues/1015#issuecomment-159364419","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1015","id":159364419,"user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"created_at":"2015-11-24T18:31:38Z","updated_at":"2015-11-24T18:31:38Z","body":"ha! this is awesome. does #1190 need to go in first?"}}