{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/35962730","id":35962730,"diff_hunk":"@@ -0,0 +1,45 @@\n+package org.broadinstitute.hellbender.tools.dataflow.pipelines;\n+\n+\n+import org.broadinstitute.hellbender.CommandLineProgramTest;\n+import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;\n+import org.broadinstitute.hellbender.tools.IntegrationTestSpec;\n+import org.testng.Assert;\n+import org.testng.annotations.DataProvider;\n+import org.testng.annotations.Test;\n+\n+import java.io.File;\n+import java.io.IOException;\n+import java.util.ArrayList;\n+import java.util.Arrays;\n+import java.util.List;\n+\n+public class ReadsPreprocessingPipelineIntegrationTest extends CommandLineProgramTest {\n+\n+    @DataProvider(name = \"EndToEndTestData\")\n+    public Object[][] getEndToEndTestData() {\n+        final String testDir = publicTestDir + \"org/broadinstitute/hellbender/engine/\";\n+\n+        return new Object[][] {\n+                // This test case checks that the input and output bams are equal (which should be the case with stub tool implementations)\n+                { testDir + \"reads_data_source_test1.bam\", \"EOSt9JOVhp3jkwE\", testDir + \"feature_data_source_test.vcf\", new File(testDir + \"reads_data_source_test1.bam\") }\n+        };\n+    }\n+\n+    @Test(dataProvider = \"EndToEndTestData\", groups = {\"cloud\"})\n+    public void testPipelineEndToEnd( final String inputBam, final String reference, final String knownSites, final File expectedOutput ) throws IOException {\n+        final File output = createTempFile(\"foo\", \".bam\");","path":"src/test/java/org/broadinstitute/hellbender/tools/dataflow/pipelines/ReadsPreprocessingPipelineIntegrationTest.java","position":31,"original_position":31,"commit_id":"df23593aeeffad42160db94a714b21cfaf552fb8","original_commit_id":"df23593aeeffad42160db94a714b21cfaf552fb8","user":{"login":"davidadamsphd","id":12084283,"avatar_url":"https://avatars.githubusercontent.com/u/12084283?v=3","gravatar_id":"","url":"https://api.github.com/users/davidadamsphd","html_url":"https://github.com/davidadamsphd","followers_url":"https://api.github.com/users/davidadamsphd/followers","following_url":"https://api.github.com/users/davidadamsphd/following{/other_user}","gists_url":"https://api.github.com/users/davidadamsphd/gists{/gist_id}","starred_url":"https://api.github.com/users/davidadamsphd/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidadamsphd/subscriptions","organizations_url":"https://api.github.com/users/davidadamsphd/orgs","repos_url":"https://api.github.com/users/davidadamsphd/repos","events_url":"https://api.github.com/users/davidadamsphd/events{/privacy}","received_events_url":"https://api.github.com/users/davidadamsphd/received_events","type":"User","site_admin":false},"body":"Please pick a better name than foo.","created_at":"2015-07-31T10:29:36Z","updated_at":"2015-07-31T10:29:36Z","html_url":"https://github.com/broadinstitute/hellbender/pull/772#discussion_r35962730","pull_request_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/772","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/35962730"},"html":{"href":"https://github.com/broadinstitute/hellbender/pull/772#discussion_r35962730"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/772"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/772","id":41276343,"html_url":"https://github.com/broadinstitute/hellbender/pull/772","diff_url":"https://github.com/broadinstitute/hellbender/pull/772.diff","patch_url":"https://github.com/broadinstitute/hellbender/pull/772.patch","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/772","number":772,"state":"open","locked":false,"title":"Add an initial stub end-to-end integration test for the ReadsPreProcessingPipeline","user":{"login":"droazen","id":798637,"avatar_url":"https://avatars.githubusercontent.com/u/798637?v=3","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"body":"Just checks that the input and output bams are equal (which is still the\r\ncase for a bam with no duplicates). 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