{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/187105540","pull_request_review_id":118819040,"id":187105540,"diff_hunk":"@@ -167,9 +172,7 @@ public int getIndex() {\n             keyedReads = spanReadsByKey(indexedReads);\n         } else {\n             // sort by group and name (incurs a shuffle)\n-            JavaPairRDD<String, IndexPair<GATKRead>> keyReadPairs = indexedReads.mapToPair(read -> new Tuple2<>(ReadsKey.keyForRead(\n-                    read.getValue()), read));\n-            keyedReads = keyReadPairs.groupByKey(numReducers);\n+            throw new GATKException(\"MarkDuplicatesSparkUtils.mark() requires input reads to be queryname sorted, yet the header indicated otherwise\");","path":"src/main/java/org/broadinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSparkUtils.java","position":19,"original_position":19,"commit_id":"dc5dfaf15fd4b91507f3891b0f5267b94e5f23c4","original_commit_id":"dc5dfaf15fd4b91507f3891b0f5267b94e5f23c4","user":{"login":"jamesemery","id":16102845,"avatar_url":"https://avatars2.githubusercontent.com/u/16102845?v=4","gravatar_id":"","url":"https://api.github.com/users/jamesemery","html_url":"https://github.com/jamesemery","followers_url":"https://api.github.com/users/jamesemery/followers","following_url":"https://api.github.com/users/jamesemery/following{/other_user}","gists_url":"https://api.github.com/users/jamesemery/gists{/gist_id}","starred_url":"https://api.github.com/users/jamesemery/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jamesemery/subscriptions","organizations_url":"https://api.github.com/users/jamesemery/orgs","repos_url":"https://api.github.com/users/jamesemery/repos","events_url":"https://api.github.com/users/jamesemery/events{/privacy}","received_events_url":"https://api.github.com/users/jamesemery/received_events","type":"User","site_admin":false},"body":"done","created_at":"2018-05-09T16:54:13Z","updated_at":"2018-05-09T16:54:14Z","html_url":"https://github.com/broadinstitute/gatk/pull/4732#discussion_r187105540","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/4732","author_association":"COLLABORATOR","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/187105540"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/4732#discussion_r187105540"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/4732"}},"in_reply_to_id":186837276},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/4732","id":185559430,"html_url":"https://github.com/broadinstitute/gatk/pull/4732","diff_url":"https://github.com/broadinstitute/gatk/pull/4732.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/4732.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4732","number":4732,"state":"open","locked":false,"title":"Fixed MarkDuplicatesSpark handling of unsorted bams","user":{"login":"jamesemery","id":16102845,"avatar_url":"https://avatars2.githubusercontent.com/u/16102845?v=4","gravatar_id":"","url":"https://api.github.com/users/jamesemery","html_url":"https://github.com/jamesemery","followers_url":"https://api.github.com/users/jamesemery/followers","following_url":"https://api.github.com/users/jamesemery/following{/other_user}","gists_url":"https://api.github.com/users/jamesemery/gists{/gist_id}","starred_url":"https://api.github.com/users/jamesemery/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jamesemery/subscriptions","organizations_url":"https://api.github.com/users/jamesemery/orgs","repos_url":"https://api.github.com/users/jamesemery/repos","events_url":"https://api.github.com/users/jamesemery/events{/privacy}","received_events_url":"https://api.github.com/users/jamesemery/received_events","type":"User","site_admin":false},"body":"Added a global sort to the beginning of the tool to ensure we are always working with name grouped bams. In the future we should evaluate if alternatives that avoid sorting are necessary.  \r\n\r\nFixes  #4701","created_at":"2018-05-02T20:59:13Z","updated_at":"2018-05-09T16:54:14Z","closed_at":null,"merged_at":null,"merge_commit_sha":"88d8516b2e89512081563a8655b4f74d0f430e84","assignee":{"login":"jamesemery","id":16102845,"avatar_url":"https://avatars2.githubusercontent.com/u/16102845?v=4","gravatar_id":"","url":"https://api.github.com/users/jamesemery","html_url":"https://github.com/jamesemery","followers_url":"https://api.github.com/users/jamesemery/followers","following_url":"https://api.github.com/users/jamesemery/following{/other_user}","gists_url":"https://api.github.com/users/jamesemery/gists{/gist_id}","starred_url":"https://api.github.com/users/jamesemery/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jamesemery/subscriptions","organizations_url":"https://api.github.com/users/jamesemery/orgs","repos_url":"https://api.github.com/users/jamesemery/repos","events_url":"https://api.github.com/users/jamesemery/events{/privacy}","received_events_url":"https://api.github.com/users/jamesemery/received_events","type":"User","site_admin":false},"assignees":[{"login":"jamesemery","id":16102845,"avatar_url":"https://avatars2.githubusercontent.com/u/16102845?v=4","gravatar_id":"","url":"https://api.github.com/users/jamesemery","html_url":"https://github.com/jamesemery","followers_url":"https://api.github.com/users/jamesemery/followers","following_url":"https://api.github.com/users/jamesemery/following{/other_user}","gists_url":"https://api.github.com/users/jamesemery/gists{/gist_id}","starred_url":"https://api.github.com/users/jamesemery/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jamesemery/subscriptions","organizations_url":"https://api.github.com/users/jamesemery/orgs","repos_url":"https://api.github.com/users/jamesemery/repos","events_url":"https://api.github.com/users/jamesemery/events{/privacy}","received_events_url":"https://api.github.com/users/jamesemery/received_events","type":"User","site_admin":false}],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/4732/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/4732/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4732/comments","statuses_url":"https://api.github.com/repos/broadinstitute/gatk/statuses/dc5dfaf15fd4b91507f3891b0f5267b94e5f23c4","head":{"label":"broadinstitute:je_MDUnsortedFix","ref":"je_MDUnsortedFix","sha":"dc5dfaf15fd4b91507f3891b0f5267b94e5f23c4","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars0.githubusercontent.com/u/393552?v=4","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"repo":{"id":27452807,"name":"gatk","full_name":"broadinstitute/gatk","owner":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars0.githubusercontent.com/u/393552?v=4","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/broadinstitute/gatk","description":"Official code repository for GATK versions 4 and up","fork":false,"url":"https://api.github.com/repos/broadinstitute/gatk","forks_url":"https://api.github.com/repos/broadinstitute/gatk/forks","keys_url":"https://api.github.com/repos/broadinstitute/gatk/keys{/key_id}","collaborators_url":"https://api.github.com/repos/broadinstitute/gatk/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/broadinstitute/gatk/teams","hooks_url":"https://api.github.com/repos/broadinstitute/gatk/hooks","issue_events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/events{/number}","events_url":"https://api.github.com/repos/broadinstitute/gatk/events","assignees_url":"https://api.github.com/repos/broadinstitute/gatk/assignees{/user}","branches_url":"https://api.github.com/repos/broadinstitute/gatk/branches{/branch}","tags_url":"https://api.github.com/repos/broadinstitute/gatk/tags","blobs_url":"https://api.github.com/repos/broadinstitute/gatk/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/broadinstitute/gatk/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/broadinstitute/gatk/git/refs{/sha}","trees_url":"https://api.github.com/repos/broadinstitute/gatk/git/trees{/sha}","statuses_url":"https://api.github.com/repos/broadinstitute/gatk/statuses/{sha}","languages_url":"https://api.github.com/repos/broadinstitute/gatk/languages","stargazers_url":"https://api.github.com/repos/broadinstitute/gatk/stargazers","contributors_url":"https://api.github.com/repos/broadinstitute/gatk/contributors","subscribers_url":"https://api.github.com/repos/broadinstitute/gatk/subscribers","subscription_url":"https://api.github.com/repos/broadinstitute/gatk/subscription","commits_url":"https://api.github.com/repos/broadinstitute/gatk/commits{/sha}","git_commits_url":"https://api.github.com/repos/broadinstitute/gatk/git/commits{/sha}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/comments{/number}","issue_comment_url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments{/number}","contents_url":"https://api.github.com/repos/broadinstitute/gatk/contents/{+path}","compare_url":"https://api.github.com/repos/broadinstitute/gatk/compare/{base}...{head}","merges_url":"https://api.github.com/repos/broadinstitute/gatk/merges","archive_url":"https://api.github.com/repos/broadinstitute/gatk/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/broadinstitute/gatk/downloads","issues_url":"https://api.github.com/repos/broadinstitute/gatk/issues{/number}","pulls_url":"https://api.github.com/repos/broadinstitute/gatk/pulls{/number}","milestones_url":"https://api.github.com/repos/broadinstitute/gatk/milestones{/number}","notifications_url":"https://api.github.com/repos/broadinstitute/gatk/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/broadinstitute/gatk/labels{/name}","releases_url":"https://api.github.com/repos/broadinstitute/gatk/releases{/id}","deployments_url":"https://api.github.com/repos/broadinstitute/gatk/deployments","created_at":"2014-12-02T20:50:36Z","updated_at":"2018-05-09T05:36:37Z","pushed_at":"2018-05-09T16:41:32Z","git_url":"git://github.com/broadinstitute/gatk.git","ssh_url":"git@github.com:broadinstitute/gatk.git","clone_url":"https://github.com/broadinstitute/gatk.git","svn_url":"https://github.com/broadinstitute/gatk","homepage":"https://software.broadinstitute.org/gatk","size":225237,"stargazers_count":389,"watchers_count":389,"language":"Java","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":157,"mirror_url":null,"archived":false,"open_issues_count":916,"license":{"key":"bsd-3-clause","name":"BSD 3-Clause \"New\" or \"Revised\" License","spdx_id":"BSD-3-Clause","url":"https://api.github.com/licenses/bsd-3-clause"},"forks":157,"open_issues":916,"watchers":389,"default_branch":"master"}},"base":{"label":"broadinstitute:master","ref":"master","sha":"e331de37eee93e9e1b03656f7b1905f42c47c6af","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars0.githubusercontent.com/u/393552?v=4","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"repo":{"id":27452807,"name":"gatk","full_name":"broadinstitute/gatk","owner":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars0.githubusercontent.com/u/393552?v=4","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"https://api.github.com/users/broadinstitute/followers","following_url":"https://api.github.com/users/broadinstitute/following{/other_user}","gists_url":"https://api.github.com/users/broadinstitute/gists{/gist_id}","starred_url":"https://api.github.com/users/broadinstitute/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/broadinstitute/subscriptions","organizations_url":"https://api.github.com/users/broadinstitute/orgs","repos_url":"https://api.github.com/users/broadinstitute/repos","events_url":"https://api.github.com/users/broadinstitute/events{/privacy}","received_events_url":"https://api.github.com/users/broadinstitute/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/broadinstitute/gatk","description":"Official code repository for GATK versions 4 and up","fork":false,"url":"https://api.github.com/repos/broadinstitute/gatk","forks_url":"https://api.github.com/repos/broadinstitute/gatk/forks","keys_url":"https://api.github.com/repos/broadinstitute/gatk/keys{/key_id}","collaborators_url":"https://api.github.com/repos/broadinstitute/gatk/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/broadinstitute/gatk/teams","hooks_url":"https://api.github.com/repos/broadinstitute/gatk/hooks","issue_events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/events{/number}","events_url":"https://api.github.com/repos/broadinstitute/gatk/events","assignees_url":"https://api.github.com/repos/broadinstitute/gatk/assignees{/user}","branches_url":"https://api.github.com/repos/broadinstitute/gatk/branches{/branch}","tags_url":"https://api.github.com/repos/broadinstitute/gatk/tags","blobs_url":"https://api.github.com/repos/broadinstitute/gatk/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/broadinstitute/gatk/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/broadinstitute/gatk/git/refs{/sha}","trees_url":"https://api.github.com/repos/broadinstitute/gatk/git/trees{/sha}","statuses_url":"https://api.github.com/repos/broadinstitute/gatk/statuses/{sha}","languages_url":"https://api.github.com/repos/broadinstitute/gatk/languages","stargazers_url":"https://api.github.com/repos/broadinstitute/gatk/stargazers","contributors_url":"https://api.github.com/repos/broadinstitute/gatk/contributors","subscribers_url":"https://api.github.com/repos/broadinstitute/gatk/subscribers","subscription_url":"https://api.github.com/repos/broadinstitute/gatk/subscription","commits_url":"https://api.github.com/repos/broadinstitute/gatk/commits{/sha}","git_commits_url":"https://api.github.com/repos/broadinstitute/gatk/git/commits{/sha}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/comments{/number}","issue_comment_url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments{/number}","contents_url":"https://api.github.com/repos/broadinstitute/gatk/contents/{+path}","compare_url":"https://api.github.com/repos/broadinstitute/gatk/compare/{base}...{head}","merges_url":"https://api.github.com/repos/broadinstitute/gatk/merges","archive_url":"https://api.github.com/repos/broadinstitute/gatk/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/broadinstitute/gatk/downloads","issues_url":"https://api.github.com/repos/broadinstitute/gatk/issues{/number}","pulls_url":"https://api.github.com/repos/broadinstitute/gatk/pulls{/number}","milestones_url":"https://api.github.com/repos/broadinstitute/gatk/milestones{/number}","notifications_url":"https://api.github.com/repos/broadinstitute/gatk/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/broadinstitute/gatk/labels{/name}","releases_url":"https://api.github.com/repos/broadinstitute/gatk/releases{/id}","deployments_url":"https://api.github.com/repos/broadinstitute/gatk/deployments","created_at":"2014-12-02T20:50:36Z","updated_at":"2018-05-09T05:36:37Z","pushed_at":"2018-05-09T16:41:32Z","git_url":"git://github.com/broadinstitute/gatk.git","ssh_url":"git@github.com:broadinstitute/gatk.git","clone_url":"https://github.com/broadinstitute/gatk.git","svn_url":"https://github.com/broadinstitute/gatk","homepage":"https://software.broadinstitute.org/gatk","size":225237,"stargazers_count":389,"watchers_count":389,"language":"Java","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":157,"mirror_url":null,"archived":false,"open_issues_count":916,"license":{"key":"bsd-3-clause","name":"BSD 3-Clause \"New\" or \"Revised\" License","spdx_id":"BSD-3-Clause","url":"https://api.github.com/licenses/bsd-3-clause"},"forks":157,"open_issues":916,"watchers":389,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/4732"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/4732"},"issue":{"href":"https://api.github.com/repos/broadinstitute/gatk/issues/4732"},"comments":{"href":"https://api.github.com/repos/broadinstitute/gatk/issues/4732/comments"},"review_comments":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/4732/comments"},"review_comment":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/4732/commits"},"statuses":{"href":"https://api.github.com/repos/broadinstitute/gatk/statuses/dc5dfaf15fd4b91507f3891b0f5267b94e5f23c4"}},"author_association":"COLLABORATOR"}}
{"actor":{"display_login":"jamesemery"}}