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Tests needed to be updated to reflect the code reorg of tribble.

This commit is contained in:
Mark DePristo 2011-07-16 09:22:34 -04:00
parent e106a5e734
commit eacf205f40
2 changed files with 14 additions and 10 deletions
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21
public/java/test/org/broadinstitute/sting/WalkerTest.java
View File

@ -65,19 +65,22 @@ public class WalkerTest extends BaseTest {
throw new StingException("Found an index created for file " + resultFile + " but we can only validate VCF files. Extend this code!");
}
System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec());
Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
if ( ! indexFromOutputFile.equals(dynamicIndex) ) {
Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed. FileIndex %s vs. on-the-fly %s%n",
indexFromOutputFile.getProperties(),
dynamicIndex.getProperties()));
}
assertOnDiskIndexEqualToNewlyCreatedIndex(indexFile, name, resultFile);
}
}
public static void assertOnDiskIndexEqualToNewlyCreatedIndex(final File indexFile, final String name, final File resultFile) {
System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec());
Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
if ( ! indexFromOutputFile.equals(dynamicIndex) ) {
Assert.fail(String.format("Index on disk from indexing on the fly not equal to the index created after the run completed. FileIndex %s vs. on-the-fly %s%n",
indexFromOutputFile.getProperties(),
dynamicIndex.getProperties()));
}
}
public List<String> assertMatchingMD5s(final String name, List<File> resultFiles, List<String> expectedMD5s) {
List<String> md5s = new ArrayList<String>();

3
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
View File

@ -4,6 +4,7 @@ import org.broad.tribble.Tribble;
import org.broad.tribble.index.*;
import org.broad.tribble.iterators.CloseableTribbleIterator;
import org.broad.tribble.source.BasicFeatureSource;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.testng.Assert;
import org.testng.annotations.Test;
@ -75,7 +76,7 @@ public class IndexFactoryUnitTest {
// test that the input index is the same as the one created from the identical input file
// test that the dynamic index is the same as the output index, which is equal to the input index
Assert.assertTrue(IndexFactory.onDiskIndexEqualToNewlyCreatedIndex(outputFile, outputFileIndex, new VCFCodec()));
WalkerTest.assertOnDiskIndexEqualToNewlyCreatedIndex(outputFileIndex, "unittest", outputFile);
}
}
}