{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/517","labels_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/517/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/517/comments","events_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/517/events","html_url":"https://github.com/bigdatagenomics/adam/pull/517","id":50714430,"number":517,"title":"Adding RegionRDDFunctions","user":{"login":"tdanford","id":395608,"avatar_url":"https://avatars.githubusercontent.com/u/395608?v=3","gravatar_id":"","url":"https://api.github.com/users/tdanford","html_url":"https://github.com/tdanford","followers_url":"https://api.github.com/users/tdanford/followers","following_url":"https://api.github.com/users/tdanford/following{/other_user}","gists_url":"https://api.github.com/users/tdanford/gists{/gist_id}","starred_url":"https://api.github.com/users/tdanford/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tdanford/subscriptions","organizations_url":"https://api.github.com/users/tdanford/orgs","repos_url":"https://api.github.com/users/tdanford/repos","events_url":"https://api.github.com/users/tdanford/events{/privacy}","received_events_url":"https://api.github.com/users/tdanford/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":34,"created_at":"2014-12-02T20:27:52Z","updated_at":"2015-03-26T18:44:49Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/517","html_url":"https://github.com/bigdatagenomics/adam/pull/517","diff_url":"https://github.com/bigdatagenomics/adam/pull/517.diff","patch_url":"https://github.com/bigdatagenomics/adam/pull/517.patch"},"body":"This PR contains two commits fixing #511 and #512.  \r\n\r\nFirst, it updates ReferenceRegion so that the class doesn't extend Ordered -- rather, we providing _an_ Ordering which can be used in the same contexts (and which we can replace by other orderings, if we want to order the regions in a different way).  \r\n\r\nSecond, it provides three new RDD wrapper (*Functions) classes, around RDDs of \r\n1. ReferenceRegions\r\n2. Reference-mappable values\r\n3. Pairs whose first element is a ReferenceRegion\r\n\r\nIn each case, the wrapper class provides a standard set of operations (join, filter, groupBy, windowCounts) which operate on sets of geometric operations (and are implemented under the hood, here, with RegionJoin.partitionAndJoin).  \r\n\r\nThese PRs are necessary pre-cursors to the Mutect work that's going on over in the avocado repository."},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/comments/86664229","html_url":"https://github.com/bigdatagenomics/adam/pull/517#issuecomment-86664229","issue_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/517","id":86664229,"user":{"login":"AmplabJenkins","id":4031291,"avatar_url":"https://avatars.githubusercontent.com/u/4031291?v=3","gravatar_id":"","url":"https://api.github.com/users/AmplabJenkins","html_url":"https://github.com/AmplabJenkins","followers_url":"https://api.github.com/users/AmplabJenkins/followers","following_url":"https://api.github.com/users/AmplabJenkins/following{/other_user}","gists_url":"https://api.github.com/users/AmplabJenkins/gists{/gist_id}","starred_url":"https://api.github.com/users/AmplabJenkins/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AmplabJenkins/subscriptions","organizations_url":"https://api.github.com/users/AmplabJenkins/orgs","repos_url":"https://api.github.com/users/AmplabJenkins/repos","events_url":"https://api.github.com/users/AmplabJenkins/events{/privacy}","received_events_url":"https://api.github.com/users/AmplabJenkins/received_events","type":"User","site_admin":false},"created_at":"2015-03-26T18:44:49Z","updated_at":"2015-03-26T18:44:49Z","body":"Test FAILed.\nRefer to this link for build results (access rights to CI server needed): \nhttps://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/652/<h2>Build result: FAILURE</span></h2>GitHub pull request #517 of commit b61fc3fd0c9cf3f637502e6aed2d461169549df2 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos) in workspace /home/jenkins/workspace/ADAM-prb > git rev-parse --is-inside-work-tree # timeout=10Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/*:refs/remotes/origin/pr/* > git rev-parse origin/pr/517/merge^{commit} # timeout=10 > git branch -a --contains f381757a431f91e5a09d99550aa71b7651135898 # timeout=10 > git rev-parse remotes/origin/pr/517/merge^{commit} # timeout=10Checking out Revision f381757a431f91e5a09d99550aa71b7651135898 (origin/pr/517/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f f381757a431f91e5a09d99550aa71b7651135898First time build. Skipping changelog.Triggering ADAM-prb ? 1.0.4,centosTriggering ADAM-prb ? 2.2.0,centosTriggering ADAM-prb ? 2.3.0,centosADAM-prb ? 1.0.4,centos completed with result FAILUREADAM-prb ? 2.2.0,centos completed with result FAILUREADAM-prb ? 2.3.0,centos completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'\nTest FAILed."}}