{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/595","labels_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/595/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/595/comments","events_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/595/events","html_url":"https://github.com/broadinstitute/hellbender/pull/595","id":90453228,"number":595,"title":"ApplyBQSR: cloud tests that pass","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":"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},"milestone":null,"comments":12,"created_at":"2015-06-23T18:07:17Z","updated_at":"2015-06-25T22:27:40Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/595","html_url":"https://github.com/broadinstitute/hellbender/pull/595","diff_url":"https://github.com/broadinstitute/hellbender/pull/595.diff","patch_url":"https://github.com/broadinstitute/hellbender/pull/595.patch"},"body":"To upgrade ApplyBQSR for cloud execution I had to:\r\n\r\n(i) change the input to remove reads with the unaligned flag\r\n(ii) load the recalibration report from GCS instead of shipping it as a serialized object, because Dataflow explodes if we ship too much (error is: \"malformed JSON\").\r\n(iii) for the case of a remote execution with a local output file name, add logic to copy the output via GCS to the client's machine."},"comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/issues/comments/115418630","html_url":"https://github.com/broadinstitute/hellbender/pull/595#issuecomment-115418630","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/595","id":115418630,"user":{"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},"created_at":"2015-06-25T22:27:40Z","updated_at":"2015-06-25T22:27:40Z","body":"I give  :+1:  to merging then once travis says green.  Fixing the classpath length issue is a different issue.  "}}