{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1663","repository_url":"https://api.github.com/repos/bigdatagenomics/adam","labels_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1663/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1663/comments","events_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1663/events","html_url":"https://github.com/bigdatagenomics/adam/issues/1663","id":249244006,"number":1663,"title":"Can't merge BAM files containing the same sample","user":{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars3.githubusercontent.com/u/3752466?v=4","gravatar_id":"","url":"https://api.github.com/users/fnothaft","html_url":"https://github.com/fnothaft","followers_url":"https://api.github.com/users/fnothaft/followers","following_url":"https://api.github.com/users/fnothaft/following{/other_user}","gists_url":"https://api.github.com/users/fnothaft/gists{/gist_id}","starred_url":"https://api.github.com/users/fnothaft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnothaft/subscriptions","organizations_url":"https://api.github.com/users/fnothaft/orgs","repos_url":"https://api.github.com/users/fnothaft/repos","events_url":"https://api.github.com/users/fnothaft/events{/privacy}","received_events_url":"https://api.github.com/users/fnothaft/received_events","type":"User","site_admin":false},"labels":[{"id":66733535,"url":"https://api.github.com/repos/bigdatagenomics/adam/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars3.githubusercontent.com/u/3752466?v=4","gravatar_id":"","url":"https://api.github.com/users/fnothaft","html_url":"https://github.com/fnothaft","followers_url":"https://api.github.com/users/fnothaft/followers","following_url":"https://api.github.com/users/fnothaft/following{/other_user}","gists_url":"https://api.github.com/users/fnothaft/gists{/gist_id}","starred_url":"https://api.github.com/users/fnothaft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnothaft/subscriptions","organizations_url":"https://api.github.com/users/fnothaft/orgs","repos_url":"https://api.github.com/users/fnothaft/repos","events_url":"https://api.github.com/users/fnothaft/events{/privacy}","received_events_url":"https://api.github.com/users/fnothaft/received_events","type":"User","site_admin":false},"assignees":[{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars3.githubusercontent.com/u/3752466?v=4","gravatar_id":"","url":"https://api.github.com/users/fnothaft","html_url":"https://github.com/fnothaft","followers_url":"https://api.github.com/users/fnothaft/followers","following_url":"https://api.github.com/users/fnothaft/following{/other_user}","gists_url":"https://api.github.com/users/fnothaft/gists{/gist_id}","starred_url":"https://api.github.com/users/fnothaft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fnothaft/subscriptions","organizations_url":"https://api.github.com/users/fnothaft/orgs","repos_url":"https://api.github.com/users/fnothaft/repos","events_url":"https://api.github.com/users/fnothaft/events{/privacy}","received_events_url":"https://api.github.com/users/fnothaft/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/bigdatagenomics/adam/milestones/16","html_url":"https://github.com/bigdatagenomics/adam/milestone/16","labels_url":"https://api.github.com/repos/bigdatagenomics/adam/milestones/16/labels","id":2068939,"number":16,"title":"0.23.0","description":"","creator":{"login":"heuermh","id":35293,"avatar_url":"https://avatars2.githubusercontent.com/u/35293?v=4","gravatar_id":"","url":"https://api.github.com/users/heuermh","html_url":"https://github.com/heuermh","followers_url":"https://api.github.com/users/heuermh/followers","following_url":"https://api.github.com/users/heuermh/following{/other_user}","gists_url":"https://api.github.com/users/heuermh/gists{/gist_id}","starred_url":"https://api.github.com/users/heuermh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/heuermh/subscriptions","organizations_url":"https://api.github.com/users/heuermh/orgs","repos_url":"https://api.github.com/users/heuermh/repos","events_url":"https://api.github.com/users/heuermh/events{/privacy}","received_events_url":"https://api.github.com/users/heuermh/received_events","type":"User","site_admin":false},"open_issues":16,"closed_issues":173,"state":"open","created_at":"2016-10-13T22:02:14Z","updated_at":"2017-08-10T06:19:40Z","due_on":"2017-08-05T07:00:00Z","closed_at":null},"comments":0,"created_at":"2017-08-10T06:19:40Z","updated_at":"2017-08-10T19:09:46Z","closed_at":null,"body":"We outlawed this in our glob loader code. However, this comes up if you want to do something like load in BAM files that are split out by sample. I had a benchmarking workflow where I had split a single aligned dataset into a single file per chromosome for debug, and got this on load:\r\n\r\n```\r\nUser class threw exception: java.lang.IllegalArgumentException: requirement failed: Read group dictionary contains multiple samples with identical read group names.\r\njava.lang.IllegalArgumentException: requirement failed: Read group dictionary contains multiple samples with identical read group names.\r\n\tat scala.Predef$.require(Predef.scala:233)\r\n\tat org.bdgenomics.adam.models.RecordGroupDictionary.<init>(RecordGroupDictionary.scala:85)\r\n\tat org.bdgenomics.adam.models.RecordGroupDictionary.$plus$plus(RecordGroupDictionary.scala:97)\r\n\tat org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadBam$1$$anonfun$13.apply(ADAMContext.scala:1485)\r\n\tat org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadBam$1$$anonfun$13.apply(ADAMContext.scala:1484)\r\n```"},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/comments/321645503","html_url":"https://github.com/bigdatagenomics/adam/issues/1663#issuecomment-321645503","issue_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1663","id":321645503,"user":{"login":"heuermh","id":35293,"avatar_url":"https://avatars2.githubusercontent.com/u/35293?v=4","gravatar_id":"","url":"https://api.github.com/users/heuermh","html_url":"https://github.com/heuermh","followers_url":"https://api.github.com/users/heuermh/followers","following_url":"https://api.github.com/users/heuermh/following{/other_user}","gists_url":"https://api.github.com/users/heuermh/gists{/gist_id}","starred_url":"https://api.github.com/users/heuermh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/heuermh/subscriptions","organizations_url":"https://api.github.com/users/heuermh/orgs","repos_url":"https://api.github.com/users/heuermh/repos","events_url":"https://api.github.com/users/heuermh/events{/privacy}","received_events_url":"https://api.github.com/users/heuermh/received_events","type":"User","site_admin":false},"created_at":"2017-08-10T19:09:46Z","updated_at":"2017-08-10T19:09:46Z","body":"I may have mentioned this before, but I ran into the other case, where I have BAM files for 450 samples that all re-use the same read group names.  I didn't come up with a good way to handle this.  While including all reads from all samples in the same RDD perhaps doesn't make a lot of sense, including reads overlapping a region of interest across all samples certainly does."}}
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