{"action":"created","issue":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1439","repository_url":"https://api.github.com/repos/bigdatagenomics/adam","labels_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1439/labels{/name}","comments_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1439/comments","events_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1439/events","html_url":"https://github.com/bigdatagenomics/adam/issues/1439","id":214325468,"number":1439,"title":"FeatureRDD.apply() does not allow addition of other parameters with defaults in the case class","user":{"login":"devin-petersohn","id":10732128,"avatar_url":"https://avatars3.githubusercontent.com/u/10732128?v=3","gravatar_id":"","url":"https://api.github.com/users/devin-petersohn","html_url":"https://github.com/devin-petersohn","followers_url":"https://api.github.com/users/devin-petersohn/followers","following_url":"https://api.github.com/users/devin-petersohn/following{/other_user}","gists_url":"https://api.github.com/users/devin-petersohn/gists{/gist_id}","starred_url":"https://api.github.com/users/devin-petersohn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/devin-petersohn/subscriptions","organizations_url":"https://api.github.com/users/devin-petersohn/orgs","repos_url":"https://api.github.com/users/devin-petersohn/repos","events_url":"https://api.github.com/users/devin-petersohn/events{/privacy}","received_events_url":"https://api.github.com/users/devin-petersohn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2017-03-15T09:10:27Z","updated_at":"2017-03-15T16:08:53Z","closed_at":null,"body":"I blame Scala for this:\r\n\r\nScala will not allow us to have multiple overloaded methods to have parameters with defaults. Currently, we have a default for `storageLevel` in [FeatureRDD Line 117](https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala#L117). \r\n\r\nIn #1324 we need a default for the partition map when the objects are created shown on [Line 242 of the PR branch](https://github.com/devin-petersohn/adam/blob/partitioner/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala#L242), so I'm a little stuck. I am getting this error:\r\n\r\n`adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureRDD.scala:105: error: in object FeatureRDD, multiple overloaded alternatives of apply define default arguments`\r\n\r\nWe only have a couple of options and I don't know that I like any of them. @fnothaft @heuermh I'd love some thoughts on this."},"comment":{"url":"https://api.github.com/repos/bigdatagenomics/adam/issues/comments/286791963","html_url":"https://github.com/bigdatagenomics/adam/issues/1439#issuecomment-286791963","issue_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1439","id":286791963,"user":{"login":"heuermh","id":35293,"avatar_url":"https://avatars1.githubusercontent.com/u/35293?v=3","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":"2017-03-15T16:08:53Z","updated_at":"2017-03-15T16:08:53Z","body":"It didn't really feel right passing `storageLevel` around, especially to a constructor.  Perhaps the creation of the sequence dictionary should move to where the native file format parsing happens instead?"}}
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