{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/1745","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1745/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1745/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1745/events","html_url":"https://github.com/broadinstitute/gatk/pull/1745","id":149918380,"number":1745,"title":"BQSR add option to not compute indel recalibration tables","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},"labels":[],"state":"open","locked":false,"assignee":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.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},"milestone":null,"comments":6,"created_at":"2016-04-20T23:58:29Z","updated_at":"2016-04-21T15:12:16Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1745","html_url":"https://github.com/broadinstitute/gatk/pull/1745","diff_url":"https://github.com/broadinstitute/gatk/pull/1745.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/1745.patch"},"body":"saves 10%-20% of runtime of BaseRecalibator.\r\n\r\nIntentionally done as a conservative and optional change so that we can evaluate it properly. Analyses done in https://github.com/broadinstitute/gatk/issues/1056 show that resulting bams are identical (tested on bams up to 30GB of size so far).\r\n\r\nAdded a test for it - note that it uses a 27MB file that is not in LFS, which may be a problem. (we could switch to using the standard BAM and using -L to limit territory. Using full file takes 3-4 minutes which is too slow for testing)\r\n\r\nAlso added some utility methods to a few testing classes so that we can test this properly. Added full tests for added functionality. \r\n\r\n@lbergelson  please review "},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/212965217","html_url":"https://github.com/broadinstitute/gatk/pull/1745#issuecomment-212965217","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1745","id":212965217,"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":"2016-04-21T15:12:16Z","updated_at":"2016-04-21T15:12:16Z","body":"yes, 27MB"}}