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Test that a Tabix index is created for block-compressed output formats 

- Replace .idx and .tbi with appropriate constants
This commit is contained in:
Joel Thibault 2014-03-27 16:34:30 -04:00
parent a2d40c84ba
commit ab5634cbac
2 changed files with 64 additions and 3 deletions
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7
public/gatk-framework/src/test/java/org/broadinstitute/sting/WalkerTest.java
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@ -29,6 +29,8 @@ import org.apache.commons.lang.StringUtils;
import org.broad.tribble.Tribble;
import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.index.tabix.TabixFormat;
import org.broad.tribble.util.TabixUtils;
import org.broadinstitute.sting.gatk.CommandLineExecutable;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@ -314,8 +316,9 @@ public class WalkerTest extends BaseTest {
String ext = spec.exts == null ? ".tmp" : "." + spec.exts.get(i);
File fl = createTempFile(String.format("walktest.tmp_param.%d", i), ext);
// Mark corresponding *.idx for deletion on exit as well just in case an index is created for the temp file:
new File(fl.getAbsolutePath() + ".idx").deleteOnExit();
// Mark corresponding indices for deletion on exit as well just in case an index is created for the temp file:
new File(fl.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION).deleteOnExit();
new File(fl.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION).deleteOnExit();
tmpFiles.add(fl);
}

60
public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java
View File

@ -25,13 +25,17 @@
package org.broadinstitute.sting.utils.variant;
import org.broad.tribble.Tribble;
import org.broad.tribble.index.AbstractIndex;
import org.broad.tribble.index.ChrIndex;
import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory;
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.WalkerTest;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
import org.broadinstitute.variant.vcf.VCFCodec;
import org.testng.Assert;
import org.testng.TestException;
@ -216,7 +220,7 @@ public class VCFIntegrationTest extends WalkerTest {
spec.disableShadowBCF();
File outVCF = executeTest(name, spec).first.get(0);
File outIdx = new File(outVCF.getAbsolutePath() + ".idx");
File outIdx = new File(outVCF.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION);
final Index actualIndex = IndexFactory.loadIndex(outIdx.getAbsolutePath());
final Index expectedIndex = testSpec.getIndex(outVCF);
@ -272,4 +276,58 @@ public class VCFIntegrationTest extends WalkerTest {
LinkedHashMap<String, ChrIndex> chrIndices = (LinkedHashMap<String, ChrIndex>) f.get(index);
return chrIndices.get(chr);
}
//
//
// Block-Compressed Tabix Index Tests
//
//
private class BlockCompressedIndexCreatorTest extends TestDataProvider {
private final String extension;
private BlockCompressedIndexCreatorTest(String extension) {
super(BlockCompressedIndexCreatorTest.class);
this.extension = extension;
}
public String toString() {
return String.format("File extension %s", extension);
}
}
@DataProvider(name = "BlockCompressedIndexDataProvider")
public Object[][] blockCompressedIndexCreatorData() {
for (String suffix : VCFWriterArgumentTypeDescriptor.SUPPORTED_ZIPPED_SUFFIXES)
new BlockCompressedIndexCreatorTest(".vcf" + suffix);
return TestDataProvider.getTests(BlockCompressedIndexCreatorTest.class);
}
@Test(dataProvider = "BlockCompressedIndexDataProvider")
public void testBlockCompressedIndexCreation(BlockCompressedIndexCreatorTest testSpec) throws NoSuchFieldException, IllegalAccessException {
final String commandLine = " -T SelectVariants" +
" -R " + b37KGReference +
" --no_cmdline_in_header" +
" -L 20" +
" -V " + b37_NA12878_OMNI;
final String name = "testBlockCompressedIndexCreation: " + testSpec.toString();
File outVCF = createTempFile("testBlockCompressedIndexCreation", testSpec.extension);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine, 1, Arrays.asList(""));
spec.disableShadowBCF();
spec.setOutputFileLocation(outVCF);
executeTest(name, spec);
File outTribbleIdx = new File(outVCF.getAbsolutePath() + Tribble.STANDARD_INDEX_EXTENSION);
Assert.assertFalse(outTribbleIdx.exists(), "testBlockCompressedIndexCreation: Want Tabix index but Tribble index exists: " + outTribbleIdx);
File outTabixIdx = new File(outVCF.getAbsolutePath() + TabixUtils.STANDARD_INDEX_EXTENSION);
final Index actualIndex = IndexFactory.loadIndex(outTabixIdx.toString());
Assert.assertTrue(actualIndex instanceof TabixIndex, "testBlockCompressedIndexCreation: Want Tabix index but index is not Tabix: " + outTabixIdx);
}
}