{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/590","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/590/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/590/comments","events_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/590/events","html_url":"https://github.com/broadinstitute/hellbender/issues/590","id":90217752,"number":590,"title":"test Hellbender on CRAM","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":[{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/PRIORITY_HIGH","name":"PRIORITY_HIGH","color":"e11d21"},{"url":"https://api.github.com/repos/broadinstitute/hellbender/labels/tests","name":"tests","color":"eb6420"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-06-22T21:30:58Z","updated_at":"2015-07-20T19:08:12Z","closed_at":null,"body":"GATK4 needs to work on cram files. We need to add tests to check that we can process CRAM files and get results equivalent to BAM\r\n\r\nAt the minimum, this needs to cover adding tests for:\r\n- [ ] MarkDuplicates\r\n- [ ] BQSR\r\n- [ ] PrintReads\r\n- [ ] CountReads \r\n- [ ] CountBases\r\n- [ ] MeanQualityByCycle\r\n- [ ] QualityScoreDistribution\r\n- [ ] CalculateHsMetrics\r\n- [ ] CollectGCBiasMetrics\r\n- [ ] CollectBaseDistributionByCycle\r\n- [ ] CollectQualityYieldMetrics\r\n- [ ] CollectInsertSizeMetrics\r\n- [ ] CollectAlignmentSummaryMetrics\r\n- [ ] all picard tools in the sam package\r\n\r\nIdeally also unit/integration tests for :\r\n- [ ] HaplotypeCaller\r\n- [ ] CNV coverage collection\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/comments/122991719","html_url":"https://github.com/broadinstitute/hellbender/issues/590#issuecomment-122991719","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/590","id":122991719,"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},"created_at":"2015-07-20T19:08:12Z","updated_at":"2015-07-20T19:08:12Z","body":"Will need to figure out how to convert BAM -> CRAM in order to do this."}}