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Integration test for block-compressed VCF reading

This commit is contained in:
Joel Thibault 2014-04-11 16:20:35 -04:00
parent ce770b032a
commit bdd7024d00
1 changed files with 45 additions and 0 deletions
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45
public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java
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@ -34,6 +34,7 @@ import org.broad.tribble.index.interval.IntervalTreeIndex;
import org.broad.tribble.index.linear.LinearIndex; import org.broad.tribble.index.linear.LinearIndex;
import org.broad.tribble.index.tabix.TabixIndex; import org.broad.tribble.index.tabix.TabixIndex;
import org.broad.tribble.util.TabixUtils; import org.broad.tribble.util.TabixUtils;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
import org.broadinstitute.variant.vcf.VCFCodec; 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); 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);
}
} }