{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/511","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/511/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/511/comments","events_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/511/events","html_url":"https://github.com/broadinstitute/hellbender/pull/511","id":74519105,"number":511,"title":"CalibrationTablesBuilder","user":{"login":"jean-philippe-martin","id":10458949,"avatar_url":"https://avatars.githubusercontent.com/u/10458949?v=3","gravatar_id":"","url":"https://api.github.com/users/jean-philippe-martin","html_url":"https://github.com/jean-philippe-martin","followers_url":"https://api.github.com/users/jean-philippe-martin/followers","following_url":"https://api.github.com/users/jean-philippe-martin/following{/other_user}","gists_url":"https://api.github.com/users/jean-philippe-martin/gists{/gist_id}","starred_url":"https://api.github.com/users/jean-philippe-martin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jean-philippe-martin/subscriptions","organizations_url":"https://api.github.com/users/jean-philippe-martin/orgs","repos_url":"https://api.github.com/users/jean-philippe-martin/repos","events_url":"https://api.github.com/users/jean-philippe-martin/events{/privacy}","received_events_url":"https://api.github.com/users/jean-philippe-martin/received_events","type":"User","site_admin":false},"labels":[],"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":null,"comments":4,"created_at":"2015-05-08T22:37:22Z","updated_at":"2015-05-11T18:58:45Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/511","html_url":"https://github.com/broadinstitute/hellbender/pull/511","diff_url":"https://github.com/broadinstitute/hellbender/pull/511.diff","patch_url":"https://github.com/broadinstitute/hellbender/pull/511.patch"},"body":"This code wraps around BaseRecalibrator and presents a very basic interface (set up, add reads, teardown) that's going to be used at each Dataflow worker.\r\n\r\nChallenges here:\r\n(1) I need to convert the intervals to Features because that's what the BaseRecalibrator class uses, and SimpleInterval is not a subclass of Feature. This may change in the future.\r\n(2) BaseRecalibrator takes Features as inputs - the only simple Feature class I found I could reuse is ArtificialTestFeature. Please let me know if there is a better choice (solving (1) also solves this)\r\n(3) I didn't find code to test overlap between a SimpleInterval and a Feature. Rather than roll my own I chose to use the SimpleInterval overlap test and convert to Feature lazily instead of eagerly. This may cause an interval to be converted more than once.\r\n\r\nSo please consider this the start of a discussion on \"here is something that works, but surely there's a better way?\" I'm not so much looking for every performance opportunity, but ideally I'd like to avoid using ArtificialTestFeature if a better candidate is available.\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/comments/101017211","html_url":"https://github.com/broadinstitute/hellbender/pull/511#issuecomment-101017211","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/511","id":101017211,"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":"2015-05-11T18:58:45Z","updated_at":"2015-05-11T18:58:45Z","body":"\n[![Coverage Status](https://coveralls.io/builds/2537388/badge)](https://coveralls.io/builds/2537388)\n\nCoverage increased (+0.03%) to 70.96% when pulling **9a23cab4b06ba10f69bcbeb8126c6bd055e76f76 on CTBuilder** into **8c2d8a3942bc8c94cb6cb76f4b7e95b251f553ab on master**.\n"}}