{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/34251504","id":34251504,"diff_hunk":"@@ -53,12 +53,68 @@\n  *\n  */\n @CommandLineProgramProperties(\n-        usage = CollectSequencingArtifactMetrics.USAGE,\n-        usageShort = CollectSequencingArtifactMetrics.USAGE,\n+        usage = \"This tool examines two sources of sequencing errors, bait-bias and pre-adapter artifacts resulting \" +\n+                \"from hybrid selection protocols.  Hybrid selection enables selection of specific sequences from a pool\" +","path":"src/java/picard/analysis/artifacts/CollectSequencingArtifactMetrics.java","position":7,"original_position":7,"commit_id":"018c962f27388f778ec25de6473a7e489e56df3b","original_commit_id":"018c962f27388f778ec25de6473a7e489e56df3b","user":{"login":"vdauwera","id":2748435,"avatar_url":"https://avatars.githubusercontent.com/u/2748435?v=3","gravatar_id":"","url":"https://api.github.com/users/vdauwera","html_url":"https://github.com/vdauwera","followers_url":"https://api.github.com/users/vdauwera/followers","following_url":"https://api.github.com/users/vdauwera/following{/other_user}","gists_url":"https://api.github.com/users/vdauwera/gists{/gist_id}","starred_url":"https://api.github.com/users/vdauwera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vdauwera/subscriptions","organizations_url":"https://api.github.com/users/vdauwera/orgs","repos_url":"https://api.github.com/users/vdauwera/repos","events_url":"https://api.github.com/users/vdauwera/events{/privacy}","received_events_url":"https://api.github.com/users/vdauwera/received_events","type":"User","site_admin":false},"body":"\"from hybrid selection protocols\" -> \"from hybrid selection protocols, which are typically used for exome sequencing\" \r\n\r\n(if that's correct)","created_at":"2015-07-09T12:56:44Z","updated_at":"2015-07-09T12:56:44Z","html_url":"https://github.com/broadinstitute/picard/pull/230#discussion_r34251504","pull_request_url":"https://api.github.com/repos/broadinstitute/picard/pulls/230","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/34251504"},"html":{"href":"https://github.com/broadinstitute/picard/pull/230#discussion_r34251504"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/230"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/230","id":39490546,"html_url":"https://github.com/broadinstitute/picard/pull/230","diff_url":"https://github.com/broadinstitute/picard/pull/230.diff","patch_url":"https://github.com/broadinstitute/picard/pull/230.patch","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/230","number":230,"state":"open","locked":false,"title":"Improved documentation for Picard tools","user":{"login":"dekling","id":8260472,"avatar_url":"https://avatars.githubusercontent.com/u/8260472?v=3","gravatar_id":"","url":"https://api.github.com/users/dekling","html_url":"https://github.com/dekling","followers_url":"https://api.github.com/users/dekling/followers","following_url":"https://api.github.com/users/dekling/following{/other_user}","gists_url":"https://api.github.com/users/dekling/gists{/gist_id}","starred_url":"https://api.github.com/users/dekling/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dekling/subscriptions","organizations_url":"https://api.github.com/users/dekling/orgs","repos_url":"https://api.github.com/users/dekling/repos","events_url":"https://api.github.com/users/dekling/events{/privacy}","received_events_url":"https://api.github.com/users/dekling/received_events","type":"User","site_admin":false},"body":"Added usage examples and provided detailed explanations for metrics.","created_at":"2015-07-08T15:33:28Z","updated_at":"2015-07-09T12:56:44Z","closed_at":null,"merged_at":null,"merge_commit_sha":null,"assignee":{"login":"vdauwera","id":2748435,"avatar_url":"https://avatars.githubusercontent.com/u/2748435?v=3","gravatar_id":"","url":"https://api.github.com/users/vdauwera","html_url":"https://github.com/vdauwera","followers_url":"https://api.github.com/users/vdauwera/followers","following_url":"https://api.github.com/users/vdauwera/following{/other_user}","gists_url":"https://api.github.com/users/vdauwera/gists{/gist_id}","starred_url":"https://api.github.com/users/vdauwera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vdauwera/subscriptions","organizations_url":"https://api.github.com/users/vdauwera/orgs","repos_url":"https://api.github.com/users/vdauwera/repos","events_url":"https://api.github.com/users/vdauwera/events{/privacy}","received_events_url":"https://api.github.com/users/vdauwera/received_events","type":"User","site_admin":false},"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/picard/pulls/230/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/picard/pulls/230/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/230/comments","statuses_url":"https://api.github.com/repos/broadinstitute/picard/statuses/018c962f27388f778ec25de6473a7e489e56df3b","head":{"label":"broadinstitute:dek_docs_2","ref":"dek_docs_2","sha":"018c962f27388f778ec25de6473a7e489e56df3b","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":18225913,"name":"picard","full_name":"broadinstitute/picard","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/picard","description":"A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.","fork":false,"url":"https://api.github.com/repos/broadinstitute/picard","forks_url":"https://api.github.com/repos/broadinstitute/picard/forks","keys_url":"https://api.github.com/repos/broadinstitute/picard/keys{/key_id}","collaborators_url":"https://api.github.com/repos/broadinstitute/picard/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/broadinstitute/picard/teams","hooks_url":"https://api.github.com/repos/broadinstitute/picard/hooks","issue_events_url":"https://api.github.com/repos/broadinstitute/picard/issues/events{/number}","events_url":"https://api.github.com/repos/broadinstitute/picard/events","assignees_url":"https://api.github.com/repos/broadinstitute/picard/assignees{/user}","branches_url":"https://api.github.com/repos/broadinstitute/picard/branches{/branch}","tags_url":"https://api.github.com/repos/broadinstitute/picard/tags","blobs_url":"https://api.github.com/repos/broadinstitute/picard/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/broadinstitute/picard/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/broadinstitute/picard/git/refs{/sha}","trees_url":"https://api.github.com/repos/broadinstitute/picard/git/trees{/sha}","statuses_url":"https://api.github.com/repos/broadinstitute/picard/statuses/{sha}","languages_url":"https://api.github.com/repos/broadinstitute/picard/languages","stargazers_url":"https://api.github.com/repos/broadinstitute/picard/stargazers","contributors_url":"https://api.github.com/repos/broadinstitute/picard/contributors","subscribers_url":"https://api.github.com/repos/broadinstitute/picard/subscribers","subscription_url":"https://api.github.com/repos/broadinstitute/picard/subscription","commits_url":"https://api.github.com/repos/broadinstitute/picard/commits{/sha}","git_commits_url":"https://api.github.com/repos/broadinstitute/picard/git/commits{/sha}","comments_url":"https://api.github.com/repos/broadinstitute/picard/comments{/number}","issue_comment_url":"https://api.github.com/repos/broadinstitute/picard/issues/comments{/number}","contents_url":"https://api.github.com/repos/broadinstitute/picard/contents/{+path}","compare_url":"https://api.github.com/repos/broadinstitute/picard/compare/{base}...{head}","merges_url":"https://api.github.com/repos/broadinstitute/picard/merges","archive_url":"https://api.github.com/repos/broadinstitute/picard/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/broadinstitute/picard/downloads","issues_url":"https://api.github.com/repos/broadinstitute/picard/issues{/number}","pulls_url":"https://api.github.com/repos/broadinstitute/picard/pulls{/number}","milestones_url":"https://api.github.com/repos/broadinstitute/picard/milestones{/number}","notifications_url":"https://api.github.com/repos/broadinstitute/picard/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/broadinstitute/picard/labels{/name}","releases_url":"https://api.github.com/repos/broadinstitute/picard/releases{/id}","created_at":"2014-03-28T20:43:35Z","updated_at":"2015-07-07T06:27:11Z","pushed_at":"2015-07-08T15:33:28Z","git_url":"git://github.com/broadinstitute/picard.git","ssh_url":"git@github.com:broadinstitute/picard.git","clone_url":"https://github.com/broadinstitute/picard.git","svn_url":"https://github.com/broadinstitute/picard","homepage":"http://broadinstitute.github.io/picard/","size":80913,"stargazers_count":97,"watchers_count":97,"language":"Java","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":63,"mirror_url":null,"open_issues_count":25,"forks":63,"open_issues":25,"watchers":97,"default_branch":"master"}},"base":{"label":"broadinstitute:master","ref":"master","sha":"83ec44e03ec8d07ef180ef86b7a62d59a80dedd3","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":18225913,"name":"picard","full_name":"broadinstitute/picard","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/picard","description":"A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.","fork":false,"url":"https://api.github.com/repos/broadinstitute/picard","forks_url":"https://api.github.com/repos/broadinstitute/picard/forks","keys_url":"https://api.github.com/repos/broadinstitute/picard/keys{/key_id}","collaborators_url":"https://api.github.com/repos/broadinstitute/picard/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/broadinstitute/picard/teams","hooks_url":"https://api.github.com/repos/broadinstitute/picard/hooks","issue_events_url":"https://api.github.com/repos/broadinstitute/picard/issues/events{/number}","events_url":"https://api.github.com/repos/broadinstitute/picard/events","assignees_url":"https://api.github.com/repos/broadinstitute/picard/assignees{/user}","branches_url":"https://api.github.com/repos/broadinstitute/picard/branches{/branch}","tags_url":"https://api.github.com/repos/broadinstitute/picard/tags","blobs_url":"https://api.github.com/repos/broadinstitute/picard/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/broadinstitute/picard/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/broadinstitute/picard/git/refs{/sha}","trees_url":"https://api.github.com/repos/broadinstitute/picard/git/trees{/sha}","statuses_url":"https://api.github.com/repos/broadinstitute/picard/statuses/{sha}","languages_url":"https://api.github.com/repos/broadinstitute/picard/languages","stargazers_url":"https://api.github.com/repos/broadinstitute/picard/stargazers","contributors_url":"https://api.github.com/repos/broadinstitute/picard/contributors","subscribers_url":"https://api.github.com/repos/broadinstitute/picard/subscribers","subscription_url":"https://api.github.com/repos/broadinstitute/picard/subscription","commits_url":"https://api.github.com/repos/broadinstitute/picard/commits{/sha}","git_commits_url":"https://api.github.com/repos/broadinstitute/picard/git/commits{/sha}","comments_url":"https://api.github.com/repos/broadinstitute/picard/comments{/number}","issue_comment_url":"https://api.github.com/repos/broadinstitute/picard/issues/comments{/number}","contents_url":"https://api.github.com/repos/broadinstitute/picard/contents/{+path}","compare_url":"https://api.github.com/repos/broadinstitute/picard/compare/{base}...{head}","merges_url":"https://api.github.com/repos/broadinstitute/picard/merges","archive_url":"https://api.github.com/repos/broadinstitute/picard/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/broadinstitute/picard/downloads","issues_url":"https://api.github.com/repos/broadinstitute/picard/issues{/number}","pulls_url":"https://api.github.com/repos/broadinstitute/picard/pulls{/number}","milestones_url":"https://api.github.com/repos/broadinstitute/picard/milestones{/number}","notifications_url":"https://api.github.com/repos/broadinstitute/picard/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/broadinstitute/picard/labels{/name}","releases_url":"https://api.github.com/repos/broadinstitute/picard/releases{/id}","created_at":"2014-03-28T20:43:35Z","updated_at":"2015-07-07T06:27:11Z","pushed_at":"2015-07-08T15:33:28Z","git_url":"git://github.com/broadinstitute/picard.git","ssh_url":"git@github.com:broadinstitute/picard.git","clone_url":"https://github.com/broadinstitute/picard.git","svn_url":"https://github.com/broadinstitute/picard","homepage":"http://broadinstitute.github.io/picard/","size":80913,"stargazers_count":97,"watchers_count":97,"language":"Java","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":63,"mirror_url":null,"open_issues_count":25,"forks":63,"open_issues":25,"watchers":97,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/230"},"html":{"href":"https://github.com/broadinstitute/picard/pull/230"},"issue":{"href":"https://api.github.com/repos/broadinstitute/picard/issues/230"},"comments":{"href":"https://api.github.com/repos/broadinstitute/picard/issues/230/comments"},"review_comments":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/230/comments"},"review_comment":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/230/commits"},"statuses":{"href":"https://api.github.com/repos/broadinstitute/picard/statuses/018c962f27388f778ec25de6473a7e489e56df3b"}}}}