{"action":"created","issue":{"url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/138","labels_url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/138/labels{/name}","comments_url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/138/comments","events_url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/138/events","html_url":"https://github.com/googlegenomics/dataflow-java/issues/138","id":101913364,"number":138,"title":"Update CountReads to unblock upgrade to DataflowSDK 1.0.0","user":{"login":"deflaux","id":1395500,"avatar_url":"https://avatars.githubusercontent.com/u/1395500?v=3","gravatar_id":"","url":"https://api.github.com/users/deflaux","html_url":"https://github.com/deflaux","followers_url":"https://api.github.com/users/deflaux/followers","following_url":"https://api.github.com/users/deflaux/following{/other_user}","gists_url":"https://api.github.com/users/deflaux/gists{/gist_id}","starred_url":"https://api.github.com/users/deflaux/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deflaux/subscriptions","organizations_url":"https://api.github.com/users/deflaux/orgs","repos_url":"https://api.github.com/users/deflaux/repos","events_url":"https://api.github.com/users/deflaux/events{/privacy}","received_events_url":"https://api.github.com/users/deflaux/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"iliat","id":4410767,"avatar_url":"https://avatars.githubusercontent.com/u/4410767?v=3","gravatar_id":"","url":"https://api.github.com/users/iliat","html_url":"https://github.com/iliat","followers_url":"https://api.github.com/users/iliat/followers","following_url":"https://api.github.com/users/iliat/following{/other_user}","gists_url":"https://api.github.com/users/iliat/gists{/gist_id}","starred_url":"https://api.github.com/users/iliat/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/iliat/subscriptions","organizations_url":"https://api.github.com/users/iliat/orgs","repos_url":"https://api.github.com/users/iliat/repos","events_url":"https://api.github.com/users/iliat/events{/privacy}","received_events_url":"https://api.github.com/users/iliat/received_events","type":"User","site_admin":false},"milestone":null,"comments":2,"created_at":"2015-08-19T14:57:05Z","updated_at":"2015-08-19T14:59:38Z","closed_at":null,"body":"The CountReads integration tests have a few errors such as the following due to the more strict checks in Dataflow SDK 1.0.0.  See https://github.com/googlegenomics/dataflow-java/pull/137 for related fixes in other pipelines.\r\n\r\n```\r\ncom.google.cloud.dataflow.sdk.util.IllegalMutationException: DoFn ReadFn mutated input value \r\ngs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam: chr17:41196312:41277500,\r\nlocus size = 81188, span size = 11645676 of class class com.google.cloud.genomics.dataflow.readers.bam.BAMShard (new value was \r\ngs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam: chr17:41196312:41277500,\r\nlocus size = 81188, span size = 11645676). Input values must not be mutated in any way.\r\n```"},"comment":{"url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/comments/132630092","html_url":"https://github.com/googlegenomics/dataflow-java/issues/138#issuecomment-132630092","issue_url":"https://api.github.com/repos/googlegenomics/dataflow-java/issues/138","id":132630092,"user":{"login":"deflaux","id":1395500,"avatar_url":"https://avatars.githubusercontent.com/u/1395500?v=3","gravatar_id":"","url":"https://api.github.com/users/deflaux","html_url":"https://github.com/deflaux","followers_url":"https://api.github.com/users/deflaux/followers","following_url":"https://api.github.com/users/deflaux/following{/other_user}","gists_url":"https://api.github.com/users/deflaux/gists{/gist_id}","starred_url":"https://api.github.com/users/deflaux/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/deflaux/subscriptions","organizations_url":"https://api.github.com/users/deflaux/orgs","repos_url":"https://api.github.com/users/deflaux/repos","events_url":"https://api.github.com/users/deflaux/events{/privacy}","received_events_url":"https://api.github.com/users/deflaux/received_events","type":"User","site_admin":false},"created_at":"2015-08-19T14:59:38Z","updated_at":"2015-08-19T14:59:38Z","body":"absolutely!  definitely not urgent in any way"}}