{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/42079061","id":42079061,"diff_hunk":"@@ -0,0 +1,44 @@\n+package org.broadinstitute.hellbender.tools.picard.analysis.directed;\n+        import org.broadinstitute.hellbender.CommandLineProgramTest;\n+        import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec;\n+        import org.broadinstitute.hellbender.utils.test.BaseTest;\n+        import org.testng.annotations.Test;\n+\n+        import java.io.File;\n+        import java.io.IOException;\n+\n+/**\n+ * Created by dkling on 10/14/15.\n+ */\n+\n+public final class CollectTargetedPcrMetricsIntegrationTest extends CommandLineProgramTest {\n+    private static final File TEST_DATA_PATH = new File(getTestDataDir(), \"picard/analysis/directed/CollectTargetedPcrMetrics/\");\n+\n+\n+    @Test\n+    public void testCollect () throws IOException {\n+\n+        final File input = new File(TEST_DATA_PATH, \"first5Kamod_reordered.bam\");\n+        final File amplicon_intervals = new File(TEST_DATA_PATH, \"intervals_b37_20_1.interval_list\");\n+        final File target_intervals = new File(TEST_DATA_PATH, \"intervals_b37_20_1.interval_list\");","path":"src/test/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/CollectTargetedPcrMetricsIntegrationTest.java","position":23,"original_position":23,"commit_id":"6d432c0352939cdfaa2efa22c1472780da03fcac","original_commit_id":"6d432c0352939cdfaa2efa22c1472780da03fcac","user":{"login":"akiezun","id":1993519,"avatar_url":"https://avatars.githubusercontent.com/u/1993519?v=3","gravatar_id":"","url":"https://api.github.com/users/akiezun","html_url":"https://github.com/akiezun","followers_url":"https://api.github.com/users/akiezun/followers","following_url":"https://api.github.com/users/akiezun/following{/other_user}","gists_url":"https://api.github.com/users/akiezun/gists{/gist_id}","starred_url":"https://api.github.com/users/akiezun/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/akiezun/subscriptions","organizations_url":"https://api.github.com/users/akiezun/orgs","repos_url":"https://api.github.com/users/akiezun/repos","events_url":"https://api.github.com/users/akiezun/events{/privacy}","received_events_url":"https://api.github.com/users/akiezun/received_events","type":"User","site_admin":false},"body":"I;d prefer to use a different list for amplicons and for targets - something more similar to reality of such data.","created_at":"2015-10-15T02:58:11Z","updated_at":"2015-10-15T02:58:11Z","html_url":"https://github.com/broadinstitute/gatk/pull/996#discussion_r42079061","pull_request_url":"https://api.github.com/repos/broadinstitute/gatk/pulls/996","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/42079061"},"html":{"href":"https://github.com/broadinstitute/gatk/pull/996#discussion_r42079061"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/gatk/pulls/996"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/996","id":47702270,"html_url":"https://github.com/broadinstitute/gatk/pull/996","diff_url":"https://github.com/broadinstitute/gatk/pull/996.diff","patch_url":"https://github.com/broadinstitute/gatk/pull/996.patch","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/996","number":996,"state":"open","locked":false,"title":"Dek collect targeted pcr metrics it3","user":{"login":"dekling","id":8260472,"avatar_url":"https://avatars.githubusercontent.com/u/8260472?v=3","gravatar_id":"","url":"https://api.github.com/users/dekling","html_url":"https://github.com/dekling","followers_url":"https://api.github.com/users/dekling/followers","following_url":"https://api.github.com/users/dekling/following{/other_user}","gists_url":"https://api.github.com/users/dekling/gists{/gist_id}","starred_url":"https://api.github.com/users/dekling/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dekling/subscriptions","organizations_url":"https://api.github.com/users/dekling/orgs","repos_url":"https://api.github.com/users/dekling/repos","events_url":"https://api.github.com/users/dekling/events{/privacy}","received_events_url":"https://api.github.com/users/dekling/received_events","type":"User","site_admin":false},"body":"Created new branch (old one was problematic).  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