payload: {"action":"closed","number":5399,"pull_request":{"url":"https://api.github.com/repos/hail-is/hail/pulls/5399","id":254761257,"node_id":"MDExOlB1bGxSZXF1ZXN0MjU0NzYxMjU3","html_url":"https://github.com/hail-is/hail/pull/5399","diff_url":"https://github.com/hail-is/hail/pull/5399.diff","patch_url":"https://github.com/hail-is/hail/pull/5399.patch","issue_url":"https://api.github.com/repos/hail-is/hail/issues/5399","number":5399,"state":"closed","locked":false,"title":"Do not overwrite present entries in densify","user":{"login":"chrisvittal","id":15916123,"node_id":"MDQ6VXNlcjE1OTE2MTIz","avatar_url":"https://avatars0.githubusercontent.com/u/15916123?v=4","gravatar_id":"","url":"https://api.github.com/users/chrisvittal","html_url":"https://github.com/chrisvittal","followers_url":"https://api.github.com/users/chrisvittal/followers","following_url":"https://api.github.com/users/chrisvittal/following{/other_user}","gists_url":"https://api.github.com/users/chrisvittal/gists{/gist_id}","starred_url":"https://api.github.com/users/chrisvittal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chrisvittal/subscriptions","organizations_url":"https://api.github.com/users/chrisvittal/orgs","repos_url":"https://api.github.com/users/chrisvittal/repos","events_url":"https://api.github.com/users/chrisvittal/events{/privacy}","received_events_url":"https://api.github.com/users/chrisvittal/received_events","type":"User","site_admin":false},"body":"Discovered that in one of the gnomAD gvcfs, there is a ref block that overlaps a variant. We need to be able to handle this case. For now, just don't allow overwriting an entry.","created_at":"2019-02-20T19:18:27Z","updated_at":"2019-02-20T21:31:05Z","closed_at":"2019-02-20T21:31:05Z","merged_at":"2019-02-20T21:31:05Z","merge_commit_sha":"710a6c5005408be0c0e0bc7ce9461a09f3404ac3","assignee":{"login":"daniel-goldstein","id":24440116,"node_id":"MDQ6VXNlcjI0NDQwMTE2","avatar_url":"https://avatars2.githubusercontent.com/u/24440116?v=4","gravatar_id":"","url":"https://api.github.com/users/daniel-goldstein","html_url":"https://github.com/daniel-goldstein","followers_url":"https://api.github.com/users/daniel-goldstein/followers","following_url":"https://api.github.com/users/daniel-goldstein/following{/other_user}","gists_url":"https://api.github.com/users/daniel-goldstein/gists{/gist_id}","starred_url":"https://api.github.com/users/daniel-goldstein/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/daniel-goldstein/subscriptions","organizations_url":"https://api.github.com/users/daniel-goldstein/orgs","repos_url":"https://api.github.com/users/daniel-goldstein/repos","events_url":"https://api.github.com/users/daniel-goldstein/events{/privacy}","received_events_url":"https://api.github.com/users/daniel-goldstein/received_events","type":"User","site_admin":false},"assignees":[{"login":"daniel-goldstein","id":24440116,"node_id":"MDQ6VXNlcjI0NDQwMTE2","avatar_url":"https://avatars2.githubusercontent.com/u/24440116?v=4","gravatar_id":"","url":"https://api.github.com/users/daniel-goldstein","html_url":"https://github.com/daniel-goldstein","followers_url":"https://api.github.com/users/daniel-goldstein/followers","following_url":"https://api.github.com/users/daniel-goldstein/following{/other_user}","gists_url":"https://api.github.com/users/daniel-goldstein/gists{/gist_id}","starred_url":"https://api.github.com/users/daniel-goldstein/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/daniel-goldstein/subscriptions","organizations_url":"https://api.github.com/users/daniel-goldstein/orgs","repos_url":"https://api.github.com/users/daniel-goldstein/repos","events_url":"https://api.github.com/users/daniel-goldstein/events{/privacy}","received_events_url":"https://api.github.com/users/daniel-goldstein/received_events","type":"User","site_admin":false}],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/hail-is/hail/pulls/5399/commits","review_comments_url":"https://api.github.com/repos/hail-is/hail/pulls/5399/comments","review_comment_url":"https://api.github.com/repos/hail-is/hail/pulls/comments{/number}","comments_url":"https://api.github.com/repos/hail-is/hail/issues/5399/comments","statuses_url":"https://api.github.com/repos/hail-is/hail/statuses/3cbba6728bfa9bd426ff87d563f3ece387dc894c","head":{"label":"chrisvittal:densify-do-not-overwrite","ref":"densify-do-not-overwrite","sha":"3cbba6728bfa9bd426ff87d563f3ece387dc894c","user":{"login":"chrisvittal","id":15916123,"node_id":"MDQ6VXNlcjE1OTE2MTIz","avatar_url":"https://avatars0.githubusercontent.com/u/15916123?v=4","gravatar_id":"","url":"https://api.github.com/users/chrisvittal","html_url":"https://github.com/chrisvittal","followers_url":"https://api.github.com/users/chrisvittal/followers","following_url":"https://api.github.com/users/chrisvittal/following{/other_user}","gists_url":"https://api.github.com/users/chrisvittal/gists{/gist_id}","starred_url":"https://api.github.com/users/chrisvittal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chrisvittal/subscriptions","organizations_url":"https://api.github.com/users/chrisvittal/orgs","repos_url":"https://api.github.com/users/chrisvittal/repos","events_url":"https://api.github.com/users/chrisvittal/events{/privacy}","received_events_url":"https://api.github.com/users/chrisvittal/received_events","type":"User","site_admin":false},"repo":{"id":132908677,"node_id":"MDEwOlJlcG9zaXRvcnkxMzI5MDg2Nzc=","name":"hail","full_name":"chrisvittal/hail","private":false,"owner":{"login":"chrisvittal","id":15916123,"node_id":"MDQ6VXNlcjE1OTE2MTIz","avatar_url":"https://avatars0.githubusercontent.com/u/15916123?v=4","gravatar_id":"","url":"https://api.github.com/users/chrisvittal","html_url":"https://github.com/chrisvittal","followers_url":"https://api.github.com/users/chrisvittal/followers","following_url":"https://api.github.com/users/chrisvittal/following{/other_user}","gists_url":"https://api.github.com/users/chrisvittal/gists{/gist_id}","starred_url":"https://api.github.com/users/chrisvittal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chrisvittal/subscriptions","organizations_url":"https://api.github.com/users/chrisvittal/orgs","repos_url":"https://api.github.com/users/chrisvittal/repos","events_url":"https://api.github.com/users/chrisvittal/events{/privacy}","received_events_url":"https://api.github.com/users/chrisvittal/received_events","type":"User","site_admin":false},"html_url":"https://github.com/chrisvittal/hail","description":"Scalable genomic data analysis.","fork":true,"url":"https://api.github.com/repos/chrisvittal/hail","forks_url":"https://api.github.com/repos/chrisvittal/hail/forks","keys_url":"https://api.github.com/repos/chrisvittal/hail/keys{/key_id}","collaborators_url":"https://api.github.com/repos/chrisvittal/hail/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/chrisvittal/hail/teams","hooks_url":"https://api.github.com/repos/chrisvittal/hail/hooks","issue_events_url":"https://api.github.com/repos/chrisvittal/hail/issues/events{/number}","events_url":"https://api.github.com/repos/chrisvittal/hail/events","assignees_url":"https://api.github.com/repos/chrisvittal/hail/assignees{/user}","branches_url":"https://api.github.com/repos/chrisvittal/hail/branches{/branch}","tags_url":"https://api.github.com/repos/chrisvittal/hail/tags","blobs_url":"https://api.github.com/repos/chrisvittal/hail/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/chrisvittal/hail/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/chrisvittal/hail/git/refs{/sha}","trees_url":"https://api.github.com/repos/chrisvittal/hail/git/trees{/sha}","statuses_url":"https://api.github.com/repos/chrisvittal/hail/statuses/{sha}","languages_url":"https://api.github.com/repos/chrisvittal/hail/languages","stargazers_url":"https://api.github.com/repos/chrisvittal/hail/stargazers","contributors_url":"https://api.github.com/repos/chrisvittal/hail/contributors","subscribers_url":"https://api.github.com/repos/chrisvittal/hail/subscribers","subscription_url":"https://api.github.com/repos/chrisvittal/hail/subscription","commits_url":"https://api.github.com/repos/chrisvittal/hail/commits{/sha}","git_commits_url":"https://api.github.com/repos/chrisvittal/hail/git/commits{/sha}","comments_url":"https://api.github.com/repos/chrisvittal/hail/comments{/number}","issue_comment_url":"https://api.github.com/repos/chrisvittal/hail/issues/comments{/number}","contents_url":"https://api.github.com/repos/chrisvittal/hail/contents/{+path}","compare_url":"https://api.github.com/repos/chrisvittal/hail/compare/{base}...{head}","merges_url":"https://api.github.com/repos/chrisvittal/hail/merges","archive_url":"https://api.github.com/repos/chrisvittal/hail/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/chrisvittal/hail/downloads","issues_url":"https://api.github.com/repos/chrisvittal/hail/issues{/number}","pulls_url":"https://api.github.com/repos/chrisvittal/hail/pulls{/number}","milestones_url":"https://api.github.com/repos/chrisvittal/hail/milestones{/number}","notifications_url":"https://api.github.com/repos/chrisvittal/hail/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/chrisvittal/hail/labels{/name}","releases_url":"https://api.github.com/repos/chrisvittal/hail/releases{/id}","deployments_url":"https://api.github.com/repos/chrisvittal/hail/deployments","created_at":"2018-05-10T14:03:56Z","updated_at":"2018-12-10T19:01:21Z","pushed_at":"2019-02-20T21:26:21Z","git_url":"git://github.com/chrisvittal/hail.git","ssh_url":"git@github.com:chrisvittal/hail.git","clone_url":"https://github.com/chrisvittal/hail.git","svn_url":"https://github.com/chrisvittal/hail","homepage":"https://hail.is","size":59926,"stargazers_count":0,"watchers_count":0,"language":"Scala","has_issues":false,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"archived":false,"open_issues_count":0,"license":{"key":"mit","name":"MIT License","spdx_id":"MIT","url":"https://api.github.com/licenses/mit","node_id":"MDc6TGljZW5zZTEz"},"forks":0,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"hail-is:master","ref":"master","sha":"04222877d2ce403b3cb44a4cadebaa4b2c2a0793","user":{"login":"hail-is","id":20861792,"node_id":"MDEyOk9yZ2FuaXphdGlvbjIwODYxNzky","avatar_url":"https://avatars1.githubusercontent.com/u/20861792?v=4","gravatar_id":"","url":"https://api.github.com/users/hail-is","html_url":"https://github.com/hail-is","followers_url":"https://api.github.com/users/hail-is/followers","following_url":"https://api.github.com/users/hail-is/following{/other_user}","gists_url":"https://api.github.com/users/hail-is/gists{/gist_id}","starred_url":"https://api.github.com/users/hail-is/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hail-is/subscriptions","organizations_url":"https://api.github.com/users/hail-is/orgs","repos_url":"https://api.github.com/users/hail-is/repos","events_url":"https://api.github.com/users/hail-is/events{/privacy}","received_events_url":"https://api.github.com/users/hail-is/received_events","type":"Organization","site_admin":false},"repo":{"id":45069467,"node_id":"MDEwOlJlcG9zaXRvcnk0NTA2OTQ2Nw==","name":"hail","full_name":"hail-is/hail","private":false,"owner":{"login":"hail-is","id":20861792,"node_id":"MDEyOk9yZ2FuaXphdGlvbjIwODYxNzky","avatar_url":"https://avatars1.githubusercontent.com/u/20861792?v=4","gravatar_id":"","url":"https://api.github.com/users/hail-is","html_url":"https://github.com/hail-is","followers_url":"https://api.github.com/users/hail-is/followers","following_url":"https://api.github.com/users/hail-is/following{/other_user}","gists_url":"https://api.github.com/users/hail-is/gists{/gist_id}","starred_url":"https://api.github.com/users/hail-is/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hail-is/subscriptions","organizations_url":"https://api.github.com/users/hail-is/orgs","repos_url":"https://api.github.com/users/hail-is/repos","events_url":"https://api.github.com/users/hail-is/events{/privacy}","received_events_url":"https://api.github.com/users/hail-is/received_events","type":"Organization","site_admin":false},"html_url":"https://github.com/hail-is/hail","description":"Scalable genomic data analysis.","fork":false,"url":"https://api.github.com/repos/hail-is/hail","forks_url":"https://api.github.com/repos/hail-is/hail/forks","keys_url":"https://api.github.com/repos/hail-is/hail/keys{/key_id}","collaborators_url":"https://api.github.com/repos/hail-is/hail/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/hail-is/hail/teams","hooks_url":"https://api.github.com/repos/hail-is/hail/hooks","issue_events_url":"https://api.github.com/repos/hail-is/hail/issues/events{/number}","events_url":"https://api.github.com/repos/hail-is/hail/events","assignees_url":"https://api.github.com/repos/hail-is/hail/assignees{/user}","branches_url":"https://api.github.com/repos/hail-is/hail/branches{/branch}","tags_url":"https://api.github.com/repos/hail-is/hail/tags","blobs_url":"https://api.github.com/repos/hail-is/hail/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/hail-is/hail/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/hail-is/hail/git/refs{/sha}","trees_url":"https://api.github.com/repos/hail-is/hail/git/trees{/sha}","statuses_url":"https://api.github.com/repos/hail-is/hail/statuses/{sha}","languages_url":"https://api.github.com/repos/hail-is/hail/languages","stargazers_url":"https://api.github.com/repos/hail-is/hail/stargazers","contributors_url":"https://api.github.com/repos/hail-is/hail/contributors","subscribers_url":"https://api.github.com/repos/hail-is/hail/subscribers","subscription_url":"https://api.github.com/repos/hail-is/hail/subscription","commits_url":"https://api.github.com/repos/hail-is/hail/commits{/sha}","git_commits_url":"https://api.github.com/repos/hail-is/hail/git/commits{/sha}","comments_url":"https://api.github.com/repos/hail-is/hail/comments{/number}","issue_comment_url":"https://api.github.com/repos/hail-is/hail/issues/comments{/number}","contents_url":"https://api.github.com/repos/hail-is/hail/contents/{+path}","compare_url":"https://api.github.com/repos/hail-is/hail/compare/{base}...{head}","merges_url":"https://api.github.com/repos/hail-is/hail/merges","archive_url":"https://api.github.com/repos/hail-is/hail/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/hail-is/hail/downloads","issues_url":"https://api.github.com/repos/hail-is/hail/issues{/number}","pulls_url":"https://api.github.com/repos/hail-is/hail/pulls{/number}","milestones_url":"https://api.github.com/repos/hail-is/hail/milestones{/number}","notifications_url":"https://api.github.com/repos/hail-is/hail/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/hail-is/hail/labels{/name}","releases_url":"https://api.github.com/repos/hail-is/hail/releases{/id}","deployments_url":"https://api.github.com/repos/hail-is/hail/deployments","created_at":"2015-10-27T20:55:42Z","updated_at":"2019-02-20T20:22:01Z","pushed_at":"2019-02-20T21:31:05Z","git_url":"git://github.com/hail-is/hail.git","ssh_url":"git@github.com:hail-is/hail.git","clone_url":"https://github.com/hail-is/hail.git","svn_url":"https://github.com/hail-is/hail","homepage":"https://hail.is","size":94064,"stargazers_count":455,"watchers_count":455,"language":"Scala","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":false,"has_pages":false,"forks_count":125,"mirror_url":null,"archived":false,"open_issues_count":194,"license":{"key":"mit","name":"MIT License","spdx_id":"MIT","url":"https://api.github.com/licenses/mit","node_id":"MDc6TGljZW5zZTEz"},"forks":125,"open_issues":194,"watchers":455,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/hail-is/hail/pulls/5399"},"html":{"href":"https://github.com/hail-is/hail/pull/5399"},"issue":{"href":"https://api.github.com/repos/hail-is/hail/issues/5399"},"comments":{"href":"https://api.github.com/repos/hail-is/hail/issues/5399/comments"},"review_comments":{"href":"https://api.github.com/repos/hail-is/hail/pulls/5399/comments"},"review_comment":{"href":"https://api.github.com/repos/hail-is/hail/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/hail-is/hail/pulls/5399/commits"},"statuses":{"href":"https://api.github.com/repos/hail-is/hail/statuses/3cbba6728bfa9bd426ff87d563f3ece387dc894c"}},"author_association":"COLLABORATOR","merged":true,"mergeable":null,"rebaseable":null,"mergeable_state":"unknown","merged_by":{"login":"danking","id":106194,"node_id":"MDQ6VXNlcjEwNjE5NA==","avatar_url":"https://avatars2.githubusercontent.com/u/106194?v=4","gravatar_id":"","url":"https://api.github.com/users/danking","html_url":"https://github.com/danking","followers_url":"https://api.github.com/users/danking/followers","following_url":"https://api.github.com/users/danking/following{/other_user}","gists_url":"https://api.github.com/users/danking/gists{/gist_id}","starred_url":"https://api.github.com/users/danking/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/danking/subscriptions","organizations_url":"https://api.github.com/users/danking/orgs","repos_url":"https://api.github.com/users/danking/repos","events_url":"https://api.github.com/users/danking/events{/privacy}","received_events_url":"https://api.github.com/users/danking/received_events","type":"User","site_admin":false},"comments":0,"review_comments":2,"maintainer_can_modify":false,"commits":2,"additions":2,"deletions":2,"changed_files":1}}
other: {"actor":{"display_login":"danking"}}