{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/comments/101197125","pull_request_review_id":21917561,"id":101197125,"diff_hunk":"@@ -24,20 +26,18 @@\n      */\n     @Test\n     public void testEvaluateMutect2() throws Exception {\n-        final String dreamDir =  publicTestDir + \"org/broadinstitute/hellbender/tools/mutect/dream/vcfs/\";\n-        List<String> vcfList = Arrays.asList(dreamDir + \"sample_1.vcf\", dreamDir + \"sample_2.vcf\", dreamDir + \"sample_3.vcf\", dreamDir + \"sample_4.vcf\");\n-        final File vcfListFile = createTempFile(\"vcfList\", \".txt\");\n+        final String dreamDir =  publicTestDir + \"org/broadinstitute/hellbender/tools/mutect/dream/\";\n         final File output = createTempFile(\"output\", \".txt\");\n-        Path file = Paths.get(vcfListFile.getAbsolutePath());\n-        Files.write(file, vcfList, Charset.forName(\"UTF-8\"));\n         final String[] args = {\n-                \"-V\", vcfListFile.toString(),\n+                \"-V\", dreamDir + \"vcfs/dream3-chr20.vcf\",","path":"src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/CountFalsePositivesTest.java","position":22,"original_position":22,"commit_id":"89244a3b668a173771e10845e4ac033b48a366dd","original_commit_id":"89244a3b668a173771e10845e4ac033b48a366dd","user":{"login":"takutosato","id":5185538,"avatar_url":"https://avatars.githubusercontent.com/u/5185538?v=3","gravatar_id":"","url":"https://api.github.com/users/takutosato","html_url":"https://github.com/takutosato","followers_url":"https://api.github.com/users/takutosato/followers","following_url":"https://api.github.com/users/takutosato/following{/other_user}","gists_url":"https://api.github.com/users/takutosato/gists{/gist_id}","starred_url":"https://api.github.com/users/takutosato/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/takutosato/subscriptions","organizations_url":"https://api.github.com/users/takutosato/orgs","repos_url":"https://api.github.com/users/takutosato/repos","events_url":"https://api.github.com/users/takutosato/events{/privacy}","received_events_url":"https://api.github.com/users/takutosato/received_events","type":"User","site_admin":false},"body":"`args` is a string array though so with a file I'd have to call `toString()`. Figured it's simpler to work directly with a string. ","created_at":"2017-02-15T03:20:54Z","updated_at":"2017-02-15T03:20:55Z","html_url":"https://github.com/broadinstitute/gatk-protected/pull/895#discussion_r101197125","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/895","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/comments/101197125"},"html":{"href":"https://github.com/broadinstitute/gatk-protected/pull/895#discussion_r101197125"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/895"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/895","id":105670655,"html_url":"https://github.com/broadinstitute/gatk-protected/pull/895","diff_url":"https://github.com/broadinstitute/gatk-protected/pull/895.diff","patch_url":"https://github.com/broadinstitute/gatk-protected/pull/895.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk-protected/issues/895","number":895,"state":"open","locked":false,"title":"CRSP specificity","user":{"login":"takutosato","id":5185538,"avatar_url":"https://avatars.githubusercontent.com/u/5185538?v=3","gravatar_id":"","url":"https://api.github.com/users/takutosato","html_url":"https://github.com/takutosato","followers_url":"https://api.github.com/users/takutosato/followers","following_url":"https://api.github.com/users/takutosato/following{/other_user}","gists_url":"https://api.github.com/users/takutosato/gists{/gist_id}","starred_url":"https://api.github.com/users/takutosato/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/takutosato/subscriptions","organizations_url":"https://api.github.com/users/takutosato/orgs","repos_url":"https://api.github.com/users/takutosato/repos","events_url":"https://api.github.com/users/takutosato/events{/privacy}","received_events_url":"https://api.github.com/users/takutosato/received_events","type":"User","site_admin":false},"body":"#877. The highlights include\r\n\r\n* general replicate validation wdl (`mutect2-replicate-validation.wdl`)\r\n* hardcode docker in `mutect2.wdl` (it's a public docker, so any user of Mutect should use this docker by default)\r\n* bring back the glob fix because the old code doesn't work in the cloud\r\n* `CountFalsePositives.java` is now a variant walker\r\n* `Concordance.java` is still beta. But it's so intertwined in the commit history I did not want to change it. 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