{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/517","repository_url":"https://api.github.com/repos/broadinstitute/picard","labels_url":"https://api.github.com/repos/broadinstitute/picard/issues/517/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/517/comments","events_url":"https://api.github.com/repos/broadinstitute/picard/issues/517/events","html_url":"https://github.com/broadinstitute/picard/pull/517","id":149309238,"number":517,"title":"Fix an error with too many open files for Multi-Tile BCLs.","user":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2016-04-19T00:23:27Z","updated_at":"2016-04-20T14:46:14Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/517","html_url":"https://github.com/broadinstitute/picard/pull/517","diff_url":"https://github.com/broadinstitute/picard/pull/517.diff","patch_url":"https://github.com/broadinstitute/picard/pull/517.patch"},"body":"Please do not merge yet, as the real-world test case is in progress, but reviews are welcome (@jacarey).\r\n\r\n### Description\r\n\r\nWhen `PerTileCycleParser` seeks to a tile, it would call `close()` on the\r\nunderlying `cycleFilesParser`, which is fine if the parser parses only a\r\nsingle tile.  When seeking to a new tile with `MultiTileBclParser`, we\r\nwant to re-use the underlying `cycleFileParser`, so the `close()` call on the\r\nunderlying iterator was commented out.  This leads to an error with \"too\r\nmany open files\", even when setting `ulimit` to 800K files.\r\n\r\nThe solution is to only call close on the underlying iterator if the\r\nbase class' (`PerTileCycleParser`) `close()` method was called, not when the\r\n`seekToTile()` method is called.\r\n\r\n### Checklist\r\n\r\n- [x] Code compiles correctly\r\n- [x] All tests passing\r\n- [ ] Failing real-world test case now succeeds."},"comment":{"url":"https://api.github.com/repos/broadinstitute/picard/issues/comments/212454550","html_url":"https://github.com/broadinstitute/picard/pull/517#issuecomment-212454550","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/517","id":212454550,"user":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"created_at":"2016-04-20T14:46:14Z","updated_at":"2016-04-20T14:46:14Z","body":"@jacarey will do, I will probably know by the end of the day."}}