{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/46884315","id":46884315,"diff_hunk":"@@ -3,22 +3,50 @@\n import org.broadinstitute.hellbender.CommandLineProgramTest;\n import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;\n import org.broadinstitute.hellbender.exceptions.UserException;\n-import org.broadinstitute.hellbender.utils.test.IntegrationTestSpec;\n-import org.broadinstitute.hellbender.utils.test.SamAssertionUtils;\n import org.broadinstitute.hellbender.utils.test.ArgumentsBuilder;\n+import org.broadinstitute.hellbender.utils.test.SamAssertionUtils;\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.Arrays;\n \n public final class PrintReadsSparkIntegrationTest extends CommandLineProgramTest {\n \n+    private static final File TEST_DATA_DIR = getTestDataDir();\n+\n     @Override\n     public String getTestedClassName() {\n         return PrintReadsSpark.class.getSimpleName();\n     }\n \n+    @DataProvider(name=\"testingDataCRAM\")\n+    public Object[][] testingDataCRAM() {\n+        return new String[][]{\n+                {\"print_reads.sorted.cram\", \".sam\", \"print_reads.fasta\"},\n+                {\"print_reads.sorted.cram\", \".bam\", \"print_reads.fasta\"},\n+                {\"print_reads.sorted.cram\", \".cram\", \"print_reads.fasta\"},\n+                {\"print_reads.sorted.sam\", \".cram\", \"print_reads.fasta\"},\n+                {\"print_reads.sorted.bam\", \".cram\", \"print_reads.fasta\"}\n+        };\n+    }\n+\n+    @Test(dataProvider=\"testingDataCRAM\")\n+    public void testFileToFileCRAM(String fileIn, String extOut, String reference) throws Exception {\n+        String samFile= fileIn;\n+        final File outFile = File.createTempFile(samFile + \".\", extOut);","path":"src/test/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSparkIntegrationTest.java","position":38,"original_position":38,"commit_id":"a136086a3b943513f098ac25fb7c7e2a4c88ae27","original_commit_id":"a136086a3b943513f098ac25fb7c7e2a4c88ae27","user":{"login":"cmnbroad","id":10062863,"avatar_url":"https://avatars.githubusercontent.com/u/10062863?v=3","gravatar_id":"","url":"https://api.github.com/users/cmnbroad","html_url":"https://github.com/cmnbroad","followers_url":"https://api.github.com/users/cmnbroad/followers","following_url":"https://api.github.com/users/cmnbroad/following{/other_user}","gists_url":"https://api.github.com/users/cmnbroad/gists{/gist_id}","starred_url":"https://api.github.com/users/cmnbroad/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmnbroad/subscriptions","organizations_url":"https://api.github.com/users/cmnbroad/orgs","repos_url":"https://api.github.com/users/cmnbroad/repos","events_url":"https://api.github.com/users/cmnbroad/events{/privacy}","received_events_url":"https://api.github.com/users/cmnbroad/received_events","type":"User","site_admin":false},"body":"I think ReadSparkSink will still output BAM encoded records to these files. 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