{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/49885359","id":49885359,"diff_hunk":"@@ -293,6 +412,130 @@ public GATKRead next()\n         private static final int MIN_EVIDENCE = 5; // minimum evidence count in a cluster\n     }\n \n+    // Class that acts as a mapper from a stream of reads to a stream of <Kmer,BreakpointId> pairs.\n+    private static final class ClusterKmerizer implements Iterator<Tuple2<Kmer,Long>>, Iterable<Tuple2<Kmer,Long>>\n+    {\n+        private static final int CLUSTER_BREAK_DISTANCE = 500;\n+\n+        public ClusterKmerizer( Integer partIdx, Iterator<GATKRead> someInputIterator, Set<Kmer> someKillSet )\n+        {\n+            inputIterator = someInputIterator;\n+            killSet = someKillSet;\n+            breakpointId = partIdx.longValue() << 32;","path":"src/main/java/org/broadinstitute/hellbender/tools/spark/sv/GatherSplitReadsSpark.java","position":null,"original_position":236,"commit_id":"23660d8307adc7ee5510b25fc4a32ac3014b62b0","original_commit_id":"d22a83df2bf654643240814f7646b5801a4dd1a2","user":{"login":"cwhelan","id":709477,"avatar_url":"https://avatars.githubusercontent.com/u/709477?v=3","gravatar_id":"","url":"https://api.github.com/users/cwhelan","html_url":"https://github.com/cwhelan","followers_url":"https://api.github.com/users/cwhelan/followers","following_url":"https://api.github.com/users/cwhelan/following{/other_user}","gists_url":"https://api.github.com/users/cwhelan/gists{/gist_id}","starred_url":"https://api.github.com/users/cwhelan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cwhelan/subscriptions","organizations_url":"https://api.github.com/users/cwhelan/orgs","repos_url":"https://api.github.com/users/cwhelan/repos","events_url":"https://api.github.com/users/cwhelan/events{/privacy}","received_events_url":"https://api.github.com/users/cwhelan/received_events","type":"User","site_admin":false},"body":"Is there only one breakpoint per partition in this scheme then?","created_at":"2016-01-15T18:15:38Z","updated_at":"2016-01-15T18:15:38Z","html_url":"https://github.com/broadinstitute/gatk/pull/1434#discussion_r49885359","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1434","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/49885359"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/1434#discussion_r49885359"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/1434"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1434","id":56061446,"html_url":"https://github.com/broadinstitute/gatk/pull/1434","diff_url":"https://github.com/broadinstitute/gatk/pull/1434.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/1434.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1434","number":1434,"state":"open","locked":false,"title":"GatherSplitReadsSpark","user":{"login":"tedsharpe","id":9284156,"avatar_url":"https://avatars.githubusercontent.com/u/9284156?v=3","gravatar_id":"","url":"https://api.github.com/users/tedsharpe","html_url":"https://github.com/tedsharpe","followers_url":"https://api.github.com/users/tedsharpe/followers","following_url":"https://api.github.com/users/tedsharpe/following{/other_user}","gists_url":"https://api.github.com/users/tedsharpe/gists{/gist_id}","starred_url":"https://api.github.com/users/tedsharpe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tedsharpe/subscriptions","organizations_url":"https://api.github.com/users/tedsharpe/orgs","repos_url":"https://api.github.com/users/tedsharpe/repos","events_url":"https://api.github.com/users/tedsharpe/events{/privacy}","received_events_url":"https://api.github.com/users/tedsharpe/received_events","type":"User","site_admin":false},"body":" 1) reads a kmer kill list (prepared by FindBadGenomicKmers),\r\n 2) finds reads that support a notion of a breakpoint (split or discordant),\r\n 3) kmerizes them for each breakpoint ignoring those kmers that are on the kill list, and then\r\n 4) passes over all the reads again, pulling out those reads containing the breakpoint-supporting kmers.\r\n 5) Finally, the reads to be assembled for each breakpoint are dumped into a FASTQ file.\r\nFindBadGenomicKmers cleanup.  More comments.  Fewer magic values.\r\nAdded unit tests for Kmer class.","created_at":"2016-01-14T16:49:32Z","updated_at":"2016-01-15T18:15:38Z","closed_at":null,"merged_at":null,"merge_commit_sha":"6281dca35ea5596daac36d3932a631e4b8f1cadb","assignee":{"login":"cwhelan","id":709477,"avatar_url":"https://avatars.githubusercontent.com/u/709477?v=3","gravatar_id":"","url":"https://api.github.com/users/cwhelan","html_url":"https://github.com/cwhelan","followers_url":"https://api.github.com/users/cwhelan/followers","following_url":"https://api.github.com/users/cwhelan/following{/other_user}","gists_url":"https://api.github.com/users/cwhelan/gists{/gist_id}","starred_url":"https://api.github.com/users/cwhelan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cwhelan/subscriptions","organizations_url":"https://api.github.com/users/cwhelan/orgs","repos_url":"https://api.github.com/users/cwhelan/repos","events_url":"https://api.github.com/users/cwhelan/events{/privacy}","received_events_url":"https://api.github.com/users/cwhelan/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1434/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/1434/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/1434/comments","statuses_url":"https://api.github.com/repos/broadinstitute/gatk/statuses/23660d8307adc7ee5510b25fc4a32ac3014b62b0","head":{"label":"broadinstitute:cww_gather_split_reads","ref":"cww_gather_split_reads","sha":"23660d8307adc7ee5510b25fc4a32ac3014b62b0","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","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://avatars.githubusercontent.com/u/393552?v=3","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":"GATK4 development","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}","created_at":"2014-12-02T20:50:36Z","updated_at":"2016-01-11T21:08:29Z","pushed_at":"2016-01-15T17:50:28Z","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":"","size":57016,"stargazers_count":43,"watchers_count":43,"language":"Java","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":18,"mirror_url":null,"open_issues_count":276,"forks":18,"open_issues":276,"watchers":43,"default_branch":"master"}},"base":{"label":"broadinstitute:sv_master","ref":"sv_master","sha":"ba65e4086734505c0307e5c20ea10da85b6da1b1","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars.githubusercontent.com/u/393552?v=3","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://avatars.githubusercontent.com/u/393552?v=3","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":"GATK4 development","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}","created_at":"2014-12-02T20:50:36Z","updated_at":"2016-01-11T21:08:29Z","pushed_at":"2016-01-15T17:50:28Z","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":"","size":57016,"stargazers_count":43,"watchers_count":43,"language":"Java","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":18,"mirror_url":null,"open_issues_count":276,"forks":18,"open_issues":276,"watchers":43,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/1434"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/1434"},"issue":{"href":"https://api.github.com/repos/broadinstitute/gatk/issues/1434"},"comments":{"href":"https://api.github.com/repos/broadinstitute/gatk/issues/1434/comments"},"review_comments":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/1434/comments"},"review_comment":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/1434/commits"},"statuses":{"href":"https://api.github.com/repos/broadinstitute/gatk/statuses/23660d8307adc7ee5510b25fc4a32ac3014b62b0"}}}}