{"action":"created","comment":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/comments/29343445","id":29343445,"diff_hunk":"@@ -17,13 +17,14 @@\n \n import htsjdk.samtools.SAMFileHeader.SortOrder;","path":"src/java/htsjdk/samtools/CRAMFileReader.java","position":2,"original_position":2,"commit_id":"da6811b72ca837092862105a444a56b89e02306c","original_commit_id":"da6811b72ca837092862105a444a56b89e02306c","user":{"login":"nh13","id":846274,"avatar_url":"https://avatars.githubusercontent.com/u/846274?v=3","gravatar_id":"","url":"https://api.github.com/users/nh13","html_url":"https://github.com/nh13","followers_url":"https://api.github.com/users/nh13/followers","following_url":"https://api.github.com/users/nh13/following{/other_user}","gists_url":"https://api.github.com/users/nh13/gists{/gist_id}","starred_url":"https://api.github.com/users/nh13/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nh13/subscriptions","organizations_url":"https://api.github.com/users/nh13/orgs","repos_url":"https://api.github.com/users/nh13/repos","events_url":"https://api.github.com/users/nh13/events{/privacy}","received_events_url":"https://api.github.com/users/nh13/received_events","type":"User","site_admin":false},"body":"There is a lot of yellow in intellij related to this file.  For example, on line 123 ```validationStringency``` could be final.  Could you fix those up within this file and others.","created_at":"2015-04-29T14:54:08Z","updated_at":"2015-04-29T14:54:08Z","html_url":"https://github.com/samtools/htsjdk/pull/224#discussion_r29343445","pull_request_url":"https://api.github.com/repos/samtools/htsjdk/pulls/224","_links":{"self":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/comments/29343445"},"html":{"href":"https://github.com/samtools/htsjdk/pull/224#discussion_r29343445"},"pull_request":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/224"}}},"pull_request":{"url":"https://api.github.com/repos/samtools/htsjdk/pulls/224","id":34062371,"html_url":"https://github.com/samtools/htsjdk/pull/224","diff_url":"https://github.com/samtools/htsjdk/pull/224.diff","patch_url":"https://github.com/samtools/htsjdk/pull/224.patch","issue_url":"https://api.github.com/repos/samtools/htsjdk/issues/224","number":224,"state":"open","locked":false,"title":"Cam3 update","user":{"login":"vadimzalunin","id":668644,"avatar_url":"https://avatars.githubusercontent.com/u/668644?v=3","gravatar_id":"","url":"https://api.github.com/users/vadimzalunin","html_url":"https://github.com/vadimzalunin","followers_url":"https://api.github.com/users/vadimzalunin/followers","following_url":"https://api.github.com/users/vadimzalunin/following{/other_user}","gists_url":"https://api.github.com/users/vadimzalunin/gists{/gist_id}","starred_url":"https://api.github.com/users/vadimzalunin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vadimzalunin/subscriptions","organizations_url":"https://api.github.com/users/vadimzalunin/orgs","repos_url":"https://api.github.com/users/vadimzalunin/repos","events_url":"https://api.github.com/users/vadimzalunin/events{/privacy}","received_events_url":"https://api.github.com/users/vadimzalunin/received_events","type":"User","site_admin":false},"body":"CRAM3, indexing and code cleaning","created_at":"2015-04-24T16:06:30Z","updated_at":"2015-04-29T14:54:08Z","closed_at":null,"merged_at":null,"merge_commit_sha":null,"assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/samtools/htsjdk/pulls/224/commits","review_comments_url":"https://api.github.com/repos/samtools/htsjdk/pulls/224/comments","review_comment_url":"https://api.github.com/repos/samtools/htsjdk/pulls/comments{/number}","comments_url":"https://api.github.com/repos/samtools/htsjdk/issues/224/comments","statuses_url":"https://api.github.com/repos/samtools/htsjdk/statuses/da6811b72ca837092862105a444a56b89e02306c","head":{"label":"samtools:cam3_update","ref":"cam3_update","sha":"da6811b72ca837092862105a444a56b89e02306c","user":{"login":"samtools","id":1518450,"avatar_url":"https://avatars.githubusercontent.com/u/1518450?v=3","gravatar_id":"","url":"https://api.github.com/users/samtools","html_url":"https://github.com/samtools","followers_url":"https://api.github.com/users/samtools/followers","following_url":"https://api.github.com/users/samtools/following{/other_user}","gists_url":"https://api.github.com/users/samtools/gists{/gist_id}","starred_url":"https://api.github.com/users/samtools/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/samtools/subscriptions","organizations_url":"https://api.github.com/users/samtools/orgs","repos_url":"https://api.github.com/users/samtools/repos","events_url":"https://api.github.com/users/samtools/events{/privacy}","received_events_url":"https://api.github.com/users/samtools/received_events","type":"Organization","site_admin":false},"repo":{"id":19272315,"name":"htsjdk","full_name":"samtools/htsjdk","owner":{"login":"samtools","id":1518450,"avatar_url":"https://avatars.githubusercontent.com/u/1518450?v=3","gravatar_id":"","url":"https://api.github.com/users/samtools","html_url":"https://github.com/samtools","followers_url":"https://api.github.com/users/samtools/followers","following_url":"https://api.github.com/users/samtools/following{/other_user}","gists_url":"https://api.github.com/users/samtools/gists{/gist_id}","starred_url":"https://api.github.com/users/samtools/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/samtools/subscriptions","organizations_url":"https://api.github.com/users/samtools/orgs","repos_url":"https://api.github.com/users/samtools/repos","events_url":"https://api.github.com/users/samtools/events{/privacy}","received_events_url":"https://api.github.com/users/samtools/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/samtools/htsjdk","description":"A Java API for high-throughput sequencing data (HTS) formats.","fork":false,"url":"https://api.github.com/repos/samtools/htsjdk","forks_url":"https://api.github.com/repos/samtools/htsjdk/forks","keys_url":"https://api.github.com/repos/samtools/htsjdk/keys{/key_id}","collaborators_url":"https://api.github.com/repos/samtools/htsjdk/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/samtools/htsjdk/teams","hooks_url":"https://api.github.com/repos/samtools/htsjdk/hooks","issue_events_url":"https://api.github.com/repos/samtools/htsjdk/issues/events{/number}","events_url":"https://api.github.com/repos/samtools/htsjdk/events","assignees_url":"https://api.github.com/repos/samtools/htsjdk/assignees{/user}","branches_url":"https://api.github.com/repos/samtools/htsjdk/branches{/branch}","tags_url":"https://api.github.com/repos/samtools/htsjdk/tags","blobs_url":"https://api.github.com/repos/samtools/htsjdk/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/samtools/htsjdk/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/samtools/htsjdk/git/refs{/sha}","trees_url":"https://api.github.com/repos/samtools/htsjdk/git/trees{/sha}","statuses_url":"https://api.github.com/repos/samtools/htsjdk/statuses/{sha}","languages_url":"https://api.github.com/repos/samtools/htsjdk/languages","stargazers_url":"https://api.github.com/repos/samtools/htsjdk/stargazers","contributors_url":"https://api.github.com/repos/samtools/htsjdk/contributors","subscribers_url":"https://api.github.com/repos/samtools/htsjdk/subscribers","subscription_url":"https://api.github.com/repos/samtools/htsjdk/subscription","commits_url":"https://api.github.com/repos/samtools/htsjdk/commits{/sha}","git_commits_url":"https://api.github.com/repos/samtools/htsjdk/git/commits{/sha}","comments_url":"https://api.github.com/repos/samtools/htsjdk/comments{/number}","issue_comment_url":"https://api.github.com/repos/samtools/htsjdk/issues/comments{/number}","contents_url":"https://api.github.com/repos/samtools/htsjdk/contents/{+path}","compare_url":"https://api.github.com/repos/samtools/htsjdk/compare/{base}...{head}","merges_url":"https://api.github.com/repos/samtools/htsjdk/merges","archive_url":"https://api.github.com/repos/samtools/htsjdk/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/samtools/htsjdk/downloads","issues_url":"https://api.github.com/repos/samtools/htsjdk/issues{/number}","pulls_url":"https://api.github.com/repos/samtools/htsjdk/pulls{/number}","milestones_url":"https://api.github.com/repos/samtools/htsjdk/milestones{/number}","notifications_url":"https://api.github.com/repos/samtools/htsjdk/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/samtools/htsjdk/labels{/name}","releases_url":"https://api.github.com/repos/samtools/htsjdk/releases{/id}","created_at":"2014-04-29T10:11:28Z","updated_at":"2015-04-28T23:18:10Z","pushed_at":"2015-04-29T12:58:17Z","git_url":"git://github.com/samtools/htsjdk.git","ssh_url":"git@github.com:samtools/htsjdk.git","clone_url":"https://github.com/samtools/htsjdk.git","svn_url":"https://github.com/samtools/htsjdk","homepage":"http://samtools.github.io/htsjdk/","size":53571,"stargazers_count":42,"watchers_count":42,"language":"Java","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":51,"mirror_url":null,"open_issues_count":43,"forks":51,"open_issues":43,"watchers":42,"default_branch":"master"}},"base":{"label":"samtools:master","ref":"master","sha":"cb4acc60ec2d3e556833a1e509acaab0d20567e2","user":{"login":"samtools","id":1518450,"avatar_url":"https://avatars.githubusercontent.com/u/1518450?v=3","gravatar_id":"","url":"https://api.github.com/users/samtools","html_url":"https://github.com/samtools","followers_url":"https://api.github.com/users/samtools/followers","following_url":"https://api.github.com/users/samtools/following{/other_user}","gists_url":"https://api.github.com/users/samtools/gists{/gist_id}","starred_url":"https://api.github.com/users/samtools/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/samtools/subscriptions","organizations_url":"https://api.github.com/users/samtools/orgs","repos_url":"https://api.github.com/users/samtools/repos","events_url":"https://api.github.com/users/samtools/events{/privacy}","received_events_url":"https://api.github.com/users/samtools/received_events","type":"Organization","site_admin":false},"repo":{"id":19272315,"name":"htsjdk","full_name":"samtools/htsjdk","owner":{"login":"samtools","id":1518450,"avatar_url":"https://avatars.githubusercontent.com/u/1518450?v=3","gravatar_id":"","url":"https://api.github.com/users/samtools","html_url":"https://github.com/samtools","followers_url":"https://api.github.com/users/samtools/followers","following_url":"https://api.github.com/users/samtools/following{/other_user}","gists_url":"https://api.github.com/users/samtools/gists{/gist_id}","starred_url":"https://api.github.com/users/samtools/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/samtools/subscriptions","organizations_url":"https://api.github.com/users/samtools/orgs","repos_url":"https://api.github.com/users/samtools/repos","events_url":"https://api.github.com/users/samtools/events{/privacy}","received_events_url":"https://api.github.com/users/samtools/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/samtools/htsjdk","description":"A Java API for high-throughput sequencing data (HTS) formats.","fork":false,"url":"https://api.github.com/repos/samtools/htsjdk","forks_url":"https://api.github.com/repos/samtools/htsjdk/forks","keys_url":"https://api.github.com/repos/samtools/htsjdk/keys{/key_id}","collaborators_url":"https://api.github.com/repos/samtools/htsjdk/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/samtools/htsjdk/teams","hooks_url":"https://api.github.com/repos/samtools/htsjdk/hooks","issue_events_url":"https://api.github.com/repos/samtools/htsjdk/issues/events{/number}","events_url":"https://api.github.com/repos/samtools/htsjdk/events","assignees_url":"https://api.github.com/repos/samtools/htsjdk/assignees{/user}","branches_url":"https://api.github.com/repos/samtools/htsjdk/branches{/branch}","tags_url":"https://api.github.com/repos/samtools/htsjdk/tags","blobs_url":"https://api.github.com/repos/samtools/htsjdk/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/samtools/htsjdk/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/samtools/htsjdk/git/refs{/sha}","trees_url":"https://api.github.com/repos/samtools/htsjdk/git/trees{/sha}","statuses_url":"https://api.github.com/repos/samtools/htsjdk/statuses/{sha}","languages_url":"https://api.github.com/repos/samtools/htsjdk/languages","stargazers_url":"https://api.github.com/repos/samtools/htsjdk/stargazers","contributors_url":"https://api.github.com/repos/samtools/htsjdk/contributors","subscribers_url":"https://api.github.com/repos/samtools/htsjdk/subscribers","subscription_url":"https://api.github.com/repos/samtools/htsjdk/subscription","commits_url":"https://api.github.com/repos/samtools/htsjdk/commits{/sha}","git_commits_url":"https://api.github.com/repos/samtools/htsjdk/git/commits{/sha}","comments_url":"https://api.github.com/repos/samtools/htsjdk/comments{/number}","issue_comment_url":"https://api.github.com/repos/samtools/htsjdk/issues/comments{/number}","contents_url":"https://api.github.com/repos/samtools/htsjdk/contents/{+path}","compare_url":"https://api.github.com/repos/samtools/htsjdk/compare/{base}...{head}","merges_url":"https://api.github.com/repos/samtools/htsjdk/merges","archive_url":"https://api.github.com/repos/samtools/htsjdk/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/samtools/htsjdk/downloads","issues_url":"https://api.github.com/repos/samtools/htsjdk/issues{/number}","pulls_url":"https://api.github.com/repos/samtools/htsjdk/pulls{/number}","milestones_url":"https://api.github.com/repos/samtools/htsjdk/milestones{/number}","notifications_url":"https://api.github.com/repos/samtools/htsjdk/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/samtools/htsjdk/labels{/name}","releases_url":"https://api.github.com/repos/samtools/htsjdk/releases{/id}","created_at":"2014-04-29T10:11:28Z","updated_at":"2015-04-28T23:18:10Z","pushed_at":"2015-04-29T12:58:17Z","git_url":"git://github.com/samtools/htsjdk.git","ssh_url":"git@github.com:samtools/htsjdk.git","clone_url":"https://github.com/samtools/htsjdk.git","svn_url":"https://github.com/samtools/htsjdk","homepage":"http://samtools.github.io/htsjdk/","size":53571,"stargazers_count":42,"watchers_count":42,"language":"Java","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":51,"mirror_url":null,"open_issues_count":43,"forks":51,"open_issues":43,"watchers":42,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/224"},"html":{"href":"https://github.com/samtools/htsjdk/pull/224"},"issue":{"href":"https://api.github.com/repos/samtools/htsjdk/issues/224"},"comments":{"href":"https://api.github.com/repos/samtools/htsjdk/issues/224/comments"},"review_comments":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/224/comments"},"review_comment":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/samtools/htsjdk/pulls/224/commits"},"statuses":{"href":"https://api.github.com/repos/samtools/htsjdk/statuses/da6811b72ca837092862105a444a56b89e02306c"}}}}