diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java index 379a2295b..83e74ce88 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java @@ -34,6 +34,7 @@ import org.broad.tribble.index.interval.IntervalTreeIndex; import org.broad.tribble.index.linear.LinearIndex; import org.broad.tribble.index.tabix.TabixIndex; import org.broad.tribble.util.TabixUtils; +import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor; import org.broadinstitute.variant.vcf.VCFCodec; @@ -330,4 +331,48 @@ public class VCFIntegrationTest extends WalkerTest { Assert.assertTrue(actualIndex instanceof TabixIndex, "testBlockCompressedIndexCreation: Want Tabix index but index is not Tabix: " + outTabixIdx); } + // + // + // Block-Compressed Input Tests + // + // + + private class BlockCompressedInputTest extends TestDataProvider { + private final String extension; + + private BlockCompressedInputTest(String extension) { + super(BlockCompressedInputTest.class); + + this.extension = extension; + } + + public String toString() { + return String.format("File extension %s", extension); + } + } + + @DataProvider(name = "BlockCompressedInputDataProvider") + public Object[][] blockCompressedInputData() { + for (String suffix : VCFWriterArgumentTypeDescriptor.SUPPORTED_ZIPPED_SUFFIXES) + new BlockCompressedInputTest(".vcf" + suffix); + + return TestDataProvider.getTests(BlockCompressedInputTest.class); + } + + @Test(dataProvider = "BlockCompressedInputDataProvider") + public void testBlockCompressedInput(BlockCompressedInputTest testSpec) { + + File inputFile = new File(BaseTest.privateTestDir, "block_compressed_input_test" + testSpec.extension); + final String commandLine = " -T SelectVariants" + + " -R " + b37KGReference + + " --no_cmdline_in_header" + + " -V " + inputFile + + " -o %s "; + final String name = "testBlockCompressedInput: " + testSpec.toString(); + + final WalkerTestSpec spec = new WalkerTestSpec(commandLine, 1, Arrays.asList("3b60668bd973e43783d0406de80d2ed2")); + + executeTest(name, spec); + } + }