{"action":"created","comment":{"url":"https://api.github.com/repos/genome/genome/pulls/comments/28100034","id":28100034,"diff_hunk":"@@ -0,0 +1,109 @@\n+#!/usr/bin/env genome-perl\n+\n+# P R A G M A S ###############################################################\n+use strict;\n+use warnings;\n+\n+# M O D U L E S ###############################################################\n+use Test::More;\n+use Path::Class;\n+use above 'Genome';\n+#use Genome::Model::Tools::Vcf::EvaluateVcf;\n+\n+# M A I N #####################################################################\n+\n+#This is a bare minimum test that just compiles Perl and the UR class.\n+use_ok('Genome::Model::Tools::Vcf::EvaluateVcf');\n+\n+SKIP: {\n+    skip \"this is a long-running test\", 18;\n+    run_evaluate_vcf();\n+}\n+\n+done_testing();\n+\n+# S U B R O U T I N E S #######################################################\n+sub run_evaluate_vcf {\n+    my ($vcf, $gold_vcf, $roi, $true_negative_bed, $output_dir) =\n+      setup_evaluate_vcf_params();\n+\n+    my $cmd = Genome::Model::Tools::Vcf::EvaluateVcf->create(\n+        vcf               => $vcf->stringify,\n+        old_sample        => \"H_IJ-NA12878\",\n+        new_sample        => \"NA12878\",\n+        gold_vcf          => $gold_vcf->stringify,\n+        gold_sample       => \"NA12878\",\n+        roi               => $roi->stringify,\n+        true_negative_bed => $true_negative_bed->stringify,\n+        output_directory  => $output_dir->stringify,\n+    );\n+    ok($cmd, 'Got a Genome::Model::Tools::Vcf::EvaluateVcf instance');\n+    diag('executing command');\n+    ok($cmd->execute, 'successfully ran execute');\n+    my $stats = $cmd->rawstats;\n+    ok($stats, 'got the raw statistics from vcf evaluation');\n+\n+    is($cmd->stat_true_positive_found_exact(),\n+        28820, 'true_positive_found_exact passes');\n+\n+    is($cmd->stat_total_true_positive_exact(),\n+        2741358, 'total_true_positive_exact passes');\n+\n+    is($cmd->stat_sensitivity_exact(),\n+        0.0105130376988339, 'sensitivity_exact passes');","path":"lib/perl/Genome/Model/Tools/Vcf/EvaluateVcf.t","position":54,"original_position":53,"commit_id":"18a8908294694e3ca12533456c2d8f55a17b3356","original_commit_id":"355815e7dc81e5e0dac8dd66d6a58300ba8adadc","user":{"login":"indraniel","id":42710,"avatar_url":"https://avatars.githubusercontent.com/u/42710?v=3","gravatar_id":"","url":"https://api.github.com/users/indraniel","html_url":"https://github.com/indraniel","followers_url":"https://api.github.com/users/indraniel/followers","following_url":"https://api.github.com/users/indraniel/following{/other_user}","gists_url":"https://api.github.com/users/indraniel/gists{/gist_id}","starred_url":"https://api.github.com/users/indraniel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/indraniel/subscriptions","organizations_url":"https://api.github.com/users/indraniel/orgs","repos_url":"https://api.github.com/users/indraniel/repos","events_url":"https://api.github.com/users/indraniel/events{/privacy}","received_events_url":"https://api.github.com/users/indraniel/received_events","type":"User","site_admin":false},"body":"The decimal statististics does match up exactly at the moment, although this test may change in the future...","created_at":"2015-04-09T20:36:36Z","updated_at":"2015-04-09T20:36:36Z","html_url":"https://github.com/genome/genome/pull/640#discussion_r28100034","pull_request_url":"https://api.github.com/repos/genome/genome/pulls/640","_links":{"self":{"href":"https://api.github.com/repos/genome/genome/pulls/comments/28100034"},"html":{"href":"https://github.com/genome/genome/pull/640#discussion_r28100034"},"pull_request":{"href":"https://api.github.com/repos/genome/genome/pulls/640"}}},"pull_request":{"url":"https://api.github.com/repos/genome/genome/pulls/640","id":32807682,"html_url":"https://github.com/genome/genome/pull/640","diff_url":"https://github.com/genome/genome/pull/640.diff","patch_url":"https://github.com/genome/genome/pull/640.patch","issue_url":"https://api.github.com/repos/genome/genome/issues/640","number":640,"state":"open","locked":false,"title":"GMT Integration of VCF Evaluation (part 1)","user":{"login":"indraniel","id":42710,"avatar_url":"https://avatars.githubusercontent.com/u/42710?v=3","gravatar_id":"","url":"https://api.github.com/users/indraniel","html_url":"https://github.com/indraniel","followers_url":"https://api.github.com/users/indraniel/followers","following_url":"https://api.github.com/users/indraniel/following{/other_user}","gists_url":"https://api.github.com/users/indraniel/gists{/gist_id}","starred_url":"https://api.github.com/users/indraniel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/indraniel/subscriptions","organizations_url":"https://api.github.com/users/indraniel/orgs","repos_url":"https://api.github.com/users/indraniel/repos","events_url":"https://api.github.com/users/indraniel/events{/privacy}","received_events_url":"https://api.github.com/users/indraniel/received_events","type":"User","site_admin":false},"body":"This is part 1 of a 2 to 3 part roll out to integrate the [VCF Evaluation scripts][1] within the genome codebase.  The aim of this pull request is to get [evaluate_vcf.pl][2] setup as a GMT.  [evaluate_vcf.pl][2] contains the core vcf comparison algorithm.  \r\n\r\nPerformance adjustments and [additional logic][3] that work on top of the core logic will be added in future pull requests.\r\n\r\nThis pull request introduces logic that has been created and/or modified by @ernfrid, @tabbott , and @indraniel .  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https://github.com/genome/vcf-evaluation/blob/master/evaluate_vcfs.pl","created_at":"2015-04-07T21:29:50Z","updated_at":"2015-04-09T20:36:36Z","closed_at":null,"merged_at":null,"merge_commit_sha":"2c9d83704d9deababf863b9e1ef45667026cd2f9","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/genome/genome/pulls/640/commits","review_comments_url":"https://api.github.com/repos/genome/genome/pulls/640/comments","review_comment_url":"https://api.github.com/repos/genome/genome/pulls/comments{/number}","comments_url":"https://api.github.com/repos/genome/genome/issues/640/comments","statuses_url":"https://api.github.com/repos/genome/genome/statuses/18a8908294694e3ca12533456c2d8f55a17b3356","head":{"label":"indraniel:vcf-evaluate","ref":"vcf-evaluate","sha":"18a8908294694e3ca12533456c2d8f55a17b3356","user":{"login":"indraniel","id":42710,"avatar_url":"https://avatars.githubusercontent.com/u/42710?v=3","gravatar_id":"","url":"https://api.github.com/users/indraniel","html_url":"https://github.com/indraniel","followers_url":"https://api.github.com/users/indraniel/followers","following_url":"https://api.github.com/users/indraniel/following{/other_user}","gists_url":"https://api.github.com/users/indraniel/gists{/gist_id}","starred_url":"https://api.github.com/users/indraniel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/indraniel/subscriptions","organizations_url":"https://api.github.com/users/indraniel/orgs","repos_url":"https://api.github.com/users/indraniel/repos","events_url":"https://api.github.com/users/indraniel/events{/privacy}","received_events_url":"https://api.github.com/users/indraniel/received_events","type":"User","site_admin":false},"repo":{"id":23680310,"name":"genome","full_name":"indraniel/genome","owner":{"login":"indraniel","id":42710,"avatar_url":"https://avatars.githubusercontent.com/u/42710?v=3","gravatar_id":"","url":"https://api.github.com/users/indraniel","html_url":"https://github.com/indraniel","followers_url":"https://api.github.com/users/indraniel/followers","following_url":"https://api.github.com/users/indraniel/following{/other_user}","gists_url":"https://api.github.com/users/indraniel/gists{/gist_id}","starred_url":"https://api.github.com/users/indraniel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/indraniel/subscriptions","organizations_url":"https://api.github.com/users/indraniel/orgs","repos_url":"https://api.github.com/users/indraniel/repos","events_url":"https://api.github.com/users/indraniel/events{/privacy}","received_events_url":"https://api.github.com/users/indraniel/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/indraniel/genome","description":"","fork":true,"url":"https://api.github.com/repos/indraniel/genome","forks_url":"https://api.github.com/repos/indraniel/genome/forks","keys_url":"https://api.github.com/repos/indraniel/genome/keys{/key_id}","collaborators_url":"https://api.github.com/repos/indraniel/genome/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/indraniel/genome/teams","hooks_url":"https://api.github.com/repos/indraniel/genome/hooks","issue_events_url":"https://api.github.com/repos/indraniel/genome/issues/events{/number}","events_url":"https://api.github.com/repos/indraniel/genome/events","assignees_url":"https://api.github.com/repos/indraniel/genome/assignees{/user}","branches_url":"https://api.github.com/repos/indraniel/genome/branches{/branch}","tags_url":"https://api.github.com/repos/indraniel/genome/tags","blobs_url":"https://api.github.com/repos/indraniel/genome/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/indraniel/genome/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/indraniel/genome/git/refs{/sha}","trees_url":"https://api.github.com/repos/indraniel/genome/git/trees{/sha}","statuses_url":"https://api.github.com/repos/indraniel/genome/statuses/{sha}","languages_url":"https://api.github.com/repos/indraniel/genome/languages","stargazers_url":"https://api.github.com/repos/indraniel/genome/stargazers","contributors_url":"https://api.github.com/repos/indraniel/genome/contributors","subscribers_url":"https://api.github.com/repos/indraniel/genome/subscribers","subscription_url":"https://api.github.com/repos/indraniel/genome/subscription","commits_url":"https://api.github.com/repos/indraniel/genome/commits{/sha}","git_commits_url":"https://api.github.com/repos/indraniel/genome/git/commits{/sha}","comments_url":"https://api.github.com/repos/indraniel/genome/comments{/number}","issue_comment_url":"https://api.github.com/repos/indraniel/genome/issues/comments{/number}","contents_url":"https://api.github.com/repos/indraniel/genome/contents/{+path}","compare_url":"https://api.github.com/repos/indraniel/genome/compare/{base}...{head}","merges_url":"https://api.github.com/repos/indraniel/genome/merges","archive_url":"https://api.github.com/repos/indraniel/genome/{archive_format}{/ref}","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