{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/176223233","pull_request_review_id":105889500,"id":176223233,"diff_hunk":"@@ -216,13 +216,118 @@ public void testHetSensTargeted(final double expected, final File metricsFile) t\n         final Histogram depthHistogram = histograms.get(0);\n         final Histogram qualityHistogram = histograms.get(1);\n \n-        final double [] depthDistribution = TheoreticalSensitivity.normalizeHistogram(depthHistogram);\n-        final double [] qualityDistribution = TheoreticalSensitivity.normalizeHistogram(qualityHistogram);\n+        final double[] depthDistribution = TheoreticalSensitivity.normalizeHistogram(depthHistogram);\n+        final double[] qualityDistribution = TheoreticalSensitivity.normalizeHistogram(qualityHistogram);\n \n         final int sampleSize = 1_000;\n         final double logOddsThreshold = 3.0;\n \n         final double result = TheoreticalSensitivity.hetSNPSensitivity(depthDistribution, qualityDistribution, sampleSize, logOddsThreshold);\n         Assert.assertEquals(result, expected, tolerance);\n     }\n+\n+    @DataProvider(name = \"TheoreticalSensitivityConstantDepthDataProvider\")\n+    public Object[][] fractionalAlleleSensDataProvider() {\n+        final File wgsMetricsFile = new File(TEST_DIR, \"test_Solexa-332667.wgs_metrics\");\n+        final File targetedMetricsFile = new File(TEST_DIR, \"test_25103070136.targeted_pcr_metrics\");\n+\n+        // These magic numbers come from a separate implementation of the code in R.\n+        return new Object[][]{\n+                // Expected sensitivity, metrics file, allele fraction, constant depth, sample size.\n+                {1.00, wgsMetricsFile, .5, 30, 10000},\n+                {1.00, wgsMetricsFile, .5, 30, 10000},\n+                {0.78, targetedMetricsFile, .1, 30, 10000},\n+                {0.26, targetedMetricsFile, 0.1, 10, 10000}\n+        };\n+    }\n+\n+    @Test(dataProvider = \"TheoreticalSensitivityConstantDepthDataProvider\")\n+    public void testSensitivityAtConstantDepth(final double expected, final File metricsFile, final double alleleFraction, final int depth, final int sampleSize) throws Exception {\n+        // This tests Theoretical Sensitivity assuming a uniform depth with a distribution of base quality scores.\n+        // Because this only tests sensitivity at a constant depth, we use this for testing the code at high depths.\n+        final double tolerance = 0.01;\n+        final MetricsFile Metrics = new MetricsFile();\n+        Metrics.read(new FileReader(metricsFile));\n+        final List<Histogram> histograms = Metrics.getAllHistograms();\n+        final Histogram qualityHistogram = histograms.get(1);\n+\n+        final double[] qualityDistribution = TheoreticalSensitivity.normalizeHistogram(qualityHistogram);\n+\n+        // We ensure that even using different random seeds we converge to roughly the same value.\n+        for (int i = 0;i < 3;i++) {\n+            double result = TheoreticalSensitivity.sensitivityAtConstantDepth(depth, qualityDistribution, 3, sampleSize, alleleFraction, i);\n+            Assert.assertEquals(result, expected, tolerance);\n+        }\n+    }\n+\n+    @DataProvider(name = \"TheoreticalSensitivityDataProvider\")\n+    public Object[][] arbFracSensDataProvider() {\n+        final File wgsMetricsFile = new File(TEST_DIR, \"test_Solexa-332667.wgs_metrics\");\n+\n+        // This test acts primarily as an intergration test.  The sample size of 100\n+        // is not quite large enough to converge properly, but is used for the purpose of\n+        // keeping the compute time of the tests short.\n+        return new Object[][] {\n+                {0.90, wgsMetricsFile,       .5, 100},","path":"src/test/java/picard/analysis/TheoreticalSensitivityTest.java","position":67,"original_position":67,"commit_id":"b7bd39db7cba8f6aea28d4e2669b77aa40784542","original_commit_id":"42da9af327d1768ccf7131b1779a08c6c95ba891","user":{"login":"fleharty","id":10714381,"avatar_url":"https://avatars3.githubusercontent.com/u/10714381?v=4","gravatar_id":"","url":"https://api.github.com/users/fleharty","html_url":"https://github.com/fleharty","followers_url":"https://api.github.com/users/fleharty/followers","following_url":"https://api.github.com/users/fleharty/following{/other_user}","gists_url":"https://api.github.com/users/fleharty/gists{/gist_id}","starred_url":"https://api.github.com/users/fleharty/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fleharty/subscriptions","organizations_url":"https://api.github.com/users/fleharty/orgs","repos_url":"https://api.github.com/users/fleharty/repos","events_url":"https://api.github.com/users/fleharty/events{/privacy}","received_events_url":"https://api.github.com/users/fleharty/received_events","type":"User","site_admin":false},"body":"fixed","created_at":"2018-03-21T20:14:39Z","updated_at":"2018-03-21T20:14:39Z","html_url":"https://github.com/broadinstitute/picard/pull/853#discussion_r176223233","pull_request_url":"https://api.github.com/repos/broadinstitute/picard/pulls/853","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/comments/176223233"},"html":{"href":"https://github.com/broadinstitute/picard/pull/853#discussion_r176223233"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/picard/pulls/853"}},"in_reply_to_id":127236306},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/picard/pulls/853","id":128994013,"html_url":"https://github.com/broadinstitute/picard/pull/853","diff_url":"https://github.com/broadinstitute/picard/pull/853.diff","patch_url":"https://github.com/broadinstitute/picard/pull/853.patch","issue_url":"https://api.github.com/repos/broadinstitute/picard/issues/853","number":853,"state":"open","locked":false,"title":"Add option to CollectWgsMetrics to output theoretical sensitivity at various allele fractions","user":{"login":"fleharty","id":10714381,"avatar_url":"https://avatars3.githubusercontent.com/u/10714381?v=4","gravatar_id":"","url":"https://api.github.com/users/fleharty","html_url":"https://github.com/fleharty","followers_url":"https://api.github.com/users/fleharty/followers","following_url":"https://api.github.com/users/fleharty/following{/other_user}","gists_url":"https://api.github.com/users/fleharty/gists{/gist_id}","starred_url":"https://api.github.com/users/fleharty/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fleharty/subscriptions","organizations_url":"https://api.github.com/users/fleharty/orgs","repos_url":"https://api.github.com/users/fleharty/repos","events_url":"https://api.github.com/users/fleharty/events{/privacy}","received_events_url":"https://api.github.com/users/fleharty/received_events","type":"User","site_admin":false},"body":"### Description\r\n\r\nThis adds the THEORETICAL_SENSITIVITY_OUTPUT option to CollectWgsMetrics and CollectTargetedMetrics.  This option allows a user to specify a file that will contain the theoretical sensitivities at various allele fractions.\r\n\r\nThis augments the current TheoreticalHetSensitivity so that we can now calculate theoretical sensitivities for non-germline samples.\r\n\r\n----\r\n\r\n### Checklist (never delete this)\r\n\r\nNever delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below.\r\n\r\n#### Content\r\n- [x] Added or modified tests to cover changes and any new functionality\r\n- [x] Edited the README / documentation (if applicable)\r\n- [x] All tests passing on Travis\r\n\r\n#### Review\r\n- [ ] Final thumbs-up from reviewer\r\n- [ ] Rebase, squash and reword as applicable\r\n\r\nFor more detailed guidelines, see https://github.com/broadinstitute/picard/wiki/Guidelines-for-pull-requests\r\n\r\n","created_at":"2017-07-05T15:39:45Z","updated_at":"2018-03-21T20:14:39Z","closed_at":null,"merged_at":null,"merge_commit_sha":"be0a4a2f725457ea5584c512bc3dde628b1fd1e4","assignee":{"login":"davidbenjamin","id":8438890,"avatar_url":"https://avatars3.githubusercontent.com/u/8438890?v=4","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false},"assignees":[{"login":"davidbenjamin","id":8438890,"avatar_url":"https://avatars3.githubusercontent.com/u/8438890?v=4","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false},{"login":"fleharty","id":10714381,"avatar_url":"https://avatars3.githubusercontent.com/u/10714381?v=4","gravatar_id":"","url":"https://api.github.com/users/fleharty","html_url":"https://github.com/fleharty","followers_url":"https://api.github.com/users/fleharty/followers","following_url":"https://api.github.com/users/fleharty/following{/other_user}","gists_url":"https://api.github.com/users/fleharty/gists{/gist_id}","starred_url":"https://api.github.com/users/fleharty/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fleharty/subscriptions","organizations_url":"https://api.github.com/users/fleharty/orgs","repos_url":"https://api.github.com/users/fleharty/repos","events_url":"https://api.github.com/users/fleharty/events{/privacy}","received_events_url":"https://api.github.com/users/fleharty/received_events","type":"User","site_admin":false}],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/broadinstitute/picard/pulls/853/commits","review_comments_url":"https://api.github.com/repos/broadinstitute/picard/pulls/853/comments","review_comment_url":"https://api.github.com/repos/broadinstitute/picard/pulls/comments{/number}","comments_url":"https://api.github.com/repos/broadinstitute/picard/issues/853/comments","statuses_url":"https://api.github.com/repos/broadinstitute/picard/statuses/b7bd39db7cba8f6aea28d4e2669b77aa40784542","head":{"label":"broadinstitute:mf_fractionalSensitivity","ref":"mf_fractionalSensitivity","sha":"b7bd39db7cba8f6aea28d4e2669b77aa40784542","user":{"login":"broadinstitute","id":393552,"avatar_url":"https://avatars0.githubusercontent.com/u/393552?v=4","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://avatars0.githubusercontent.com/u/393552?v=4","gravatar_id":"","url":"https://api.github.com/users/broadinstitute","html_url":"https://github.com/broadinstitute","followers_url":"ht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