{"action":"created","comment":{"url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/comments/94107974","pull_request_review_id":14638312,"id":94107974,"diff_hunk":"@@ -145,7 +145,7 @@ sealed trait AlignmentRecordRDD extends AvroReadGroupGenomicRDD[AlignmentRecord,\n    *   file was saved.\n    */\n   private[rdd] def maybeSaveBam(args: ADAMSaveAnyArgs,\n-                                isSorted: Boolean = false): Boolean = {\n+                                isSorted: Boolean = isSorted): Boolean = {","path":"adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala","position":14,"original_position":14,"commit_id":"e82b3c378567662fe2be025c0487269c50f55b6a","original_commit_id":"e82b3c378567662fe2be025c0487269c50f55b6a","user":{"login":"fnothaft","id":3752466,"avatar_url":"https://avatars.githubusercontent.com/u/3752466?v=3","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},"body":"You're right that `sorted` is the prevailing usage, BTW:\r\n\r\n```\r\nadam fnothaft$ find adam-*/src/main -name \"*.scala\" -exec grep isSorted {} \\; | wc\r\n      23     158    1295\r\nadam fnothaft$ find adam-*/src/main -name \"*.scala\" -exec grep sorted {} \\; | wc\r\n      48     463    3178\r\n```\r\n\r\nThis disparity grows if you include test sources:\r\n\r\n```\r\nadam fnothaft$ find adam-*/src -name \"*.scala\" -exec grep isSorted {} \\; | wc\r\n      30     179    1459\r\nadam fnothaft$ find adam-*/src -name \"*.scala\" -exec grep sorted {} \\; | wc\r\n     135     839    7236\r\n```","created_at":"2016-12-29T07:32:19Z","updated_at":"2016-12-29T07:32:19Z","html_url":"https://github.com/bigdatagenomics/adam/pull/1324#discussion_r94107974","pull_request_url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/1324","_links":{"self":{"href":"https://api.github.com/repos/bigdatagenomics/adam/pulls/comments/94107974"},"html":{"href":"https://github.com/bigdatagenomics/adam/pull/1324#discussion_r94107974"},"pull_request":{"href":"https://api.github.com/repos/bigdatagenomics/adam/pulls/1324"}}},"pull_request":{"url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/1324","id":99263155,"html_url":"https://github.com/bigdatagenomics/adam/pull/1324","diff_url":"https://github.com/bigdatagenomics/adam/pull/1324.diff","patch_url":"https://github.com/bigdatagenomics/adam/pull/1324.patch","issue_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1324","number":1324,"state":"open","locked":false,"title":"Efficient Joins and (re)Partitioning","user":{"login":"devin-petersohn","id":10732128,"avatar_url":"https://avatars.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},"body":"Ready for review, however still needs some (hopefully minor) work.\r\n\r\nCurrent issues:\r\n1.) Previous method changed the number of partitions based on the data, but that isn't done with new method. All failing tests related to this.\r\n2.) Joining on partitions that span multiple ReferenceRegion chromosomes. Previous method used a RangePartitioner to handle this.","created_at":"2016-12-23T16:59:20Z","updated_at":"2016-12-29T07:32:19Z","closed_at":null,"merged_at":null,"merge_commit_sha":"0b4cb7efdc8f83b73075ef80b8dda0dc3fce546d","assignee":null,"assignees":[],"milestone":null,"commits_url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/1324/commits","review_comments_url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/1324/comments","review_comment_url":"https://api.github.com/repos/bigdatagenomics/adam/pulls/comments{/number}","comments_url":"https://api.github.com/repos/bigdatagenomics/adam/issues/1324/comments","statuses_url":"https://api.github.com/repos/bigdatagenomics/adam/statuses/e82b3c378567662fe2be025c0487269c50f55b6a","head":{"label":"devin-petersohn:partitioner","ref":"partitioner","sha":"e82b3c378567662fe2be025c0487269c50f55b6a","user":{"login":"devin-petersohn","id":10732128,"avatar_url":"https://avatars.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},"repo":{"id":67724277,"name":"adam","full_name":"devin-petersohn/adam","owner":{"login":"devin-petersohn","id":10732128,"avatar_url":"https://avatars.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},"private":false,"html_url":"https://github.com/devin-petersohn/adam","description":"ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet. 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