GitHub PullRequestReviewCommentEvent at 2014-10-27 20:55:19
Repository: genome
Actor: jasonwalker80
Payload: {"action":"created","comment":{"url":"https://api.github.com/repos/genome/genome/pulls/comments/19436464","id":19436464,"diff_hunk":"@@ -116,6 +116,7 @@ EOS\n # NOTE: These are in order.\n # Please put the most recent first.\n my @PICARD_VERSIONS = (\n+    '1.123' => '/gscmnt/sata132/techd/solexa/jwalker/lib/picard-tools-1.123',","path":"lib/perl/Genome/Model/Tools/Picard.pm","position":4,"original_position":4,"commit_id":"8ab61fc7d0d35df6aab88387ef13b38a80572a06","original_commit_id":"8ab61fc7d0d35df6aab88387ef13b38a80572a06","user":{"login":"jasonwalker80","id":884229,"avatar_url":"https://avatars.githubusercontent.com/u/884229?v=2","gravatar_id":"","url":"https://api.github.com/users/jasonwalker80","html_url":"https://github.com/jasonwalker80","followers_url":"https://api.github.com/users/jasonwalker80/followers","following_url":"https://api.github.com/users/jasonwalker80/following{/other_user}","gists_url":"https://api.github.com/users/jasonwalker80/gists{/gist_id}","starred_url":"https://api.github.com/users/jasonwalker80/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jasonwalker80/subscriptions","organizations_url":"https://api.github.com/users/jasonwalker80/orgs","repos_url":"https://api.github.com/users/jasonwalker80/repos","events_url":"https://api.github.com/users/jasonwalker80/events{/privacy}","received_events_url":"https://api.github.com/users/jasonwalker80/received_events","type":"User","site_admin":false},"body":"We will. @iferguson90 any comments or ETA for when/how this will look?  I'm not sure how this will work since the changes may be necessary in multiple PRs: Ian's, this one and #142","created_at":"2014-10-27T20:55:19Z","updated_at":"2014-10-27T20:55:19Z","html_url":"https://github.com/genome/genome/pull/131#discussion_r19436464","pull_request_url":"https://api.github.com/repos/genome/genome/pulls/131","_links":{"self":{"href":"https://api.github.com/repos/genome/genome/pulls/comments/19436464"},"html":{"href":"https://github.com/genome/genome/pull/131#discussion_r19436464"},"pull_request":{"href":"https://api.github.com/repos/genome/genome/pulls/131"}}},"pull_request":{"url":"https://api.github.com/repos/genome/genome/pulls/131","id":23243428,"html_url":"https://github.com/genome/genome/pull/131","diff_url":"https://github.com/genome/genome/pull/131.diff","patch_url":"https://github.com/genome/genome/pull/131.patch","issue_url":"https://api.github.com/repos/genome/genome/issues/131","number":131,"state":"open","locked":false,"title":"Picard genotype concordance","user":{"login":"jasonwalker80","id":884229,"avatar_url":"https://avatars.githubusercontent.com/u/884229?v=2","gravatar_id":"","url":"https://api.github.com/users/jasonwalker80","html_url":"https://github.com/jasonwalker80","followers_url":"https://api.github.com/users/jasonwalker80/followers","following_url":"https://api.github.com/users/jasonwalker80/following{/other_user}","gists_url":"https://api.github.com/users/jasonwalker80/gists{/gist_id}","starred_url":"https://api.github.com/users/jasonwalker80/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jasonwalker80/subscriptions","organizations_url":"https://api.github.com/users/jasonwalker80/orgs","repos_url":"https://api.github.com/users/jasonwalker80/repos","events_url":"https://api.github.com/users/jasonwalker80/events{/privacy}","received_events_url":"https://api.github.com/users/jasonwalker80/received_events","type":"User","site_admin":false},"body":"A new command is available as of Picard 1.122 to compare two VCF files for the purpose of genotype concordance.\r\n\r\nThis PR includes the gmt wrapper with tests to run GenotypeConcordance using Picard 1.123.  @iferguson90 is currently working on the packaging of the latest version of PIcard.\r\n\r\nThis PR also contains a new RefAlign command intended to replace CompareSnpsSummary for new models that use mpileup.  Currently those CompareSnp results are all zeros since it doesn't handle the new file format.  The new command is entirely VCF 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