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Now providing more information when the index on the fly isn't equal to the one created by reading the file from disk.

This commit is contained in:
Mark DePristo 2011-07-14 15:12:28 -04:00
parent 5ffeddd3b1
commit c0bbeb23ba
1 changed files with 12 additions and 1 deletions
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13
public/java/test/org/broadinstitute/sting/WalkerTest.java
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@ -26,7 +26,9 @@
package org.broadinstitute.sting; package org.broadinstitute.sting;
import org.apache.commons.lang.StringUtils; import org.apache.commons.lang.StringUtils;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.Tribble; import org.broad.tribble.Tribble;
import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory; import org.broad.tribble.index.IndexFactory;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec; import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.gatk.CommandLineExecutable; import org.broadinstitute.sting.gatk.CommandLineExecutable;
@ -64,10 +66,19 @@ public class WalkerTest extends BaseTest {
} }
System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile); System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
Assert.assertTrue(IndexFactory.onDiskIndexEqualToNewlyCreatedIndex(resultFile, indexFile, new VCFCodec()), "Index on disk from indexing on the fly not equal to the index created after the run completed"); 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) { public List<String> assertMatchingMD5s(final String name, List<File> resultFiles, List<String> expectedMD5s) {
List<String> md5s = new ArrayList<String>(); List<String> md5s = new ArrayList<String>();
for (int i = 0; i < resultFiles.size(); i++) { for (int i = 0; i < resultFiles.size(); i++) {