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Fixed comparison of VCFHeader as the set.equals() isn't working as expected

This commit is contained in:
Mark DePristo 2012-05-31 11:20:41 -04:00
parent b0ea14ef0f
commit 8fc1a26ac7
2 changed files with 13 additions and 4 deletions
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8
public/java/test/org/broadinstitute/sting/WalkerTest.java
View File

@ -67,6 +67,7 @@ public class WalkerTest extends BaseTest {
logger.warn("Checking shadow BCF output file " + bcfFile + " against VCF file " + resultFile); logger.warn("Checking shadow BCF output file " + bcfFile + " against VCF file " + resultFile);
try { try {
VariantContextTestProvider.assertVCFandBCFFilesAreTheSame(resultFile, bcfFile); VariantContextTestProvider.assertVCFandBCFFilesAreTheSame(resultFile, bcfFile);
logger.warn(" Shadow BCF PASSED!");
} catch ( Exception e ) { } catch ( Exception e ) {
Assert.fail("Exception received reading shadow BCFFile " + bcfFile + " for test " + name, e); Assert.fail("Exception received reading shadow BCFFile " + bcfFile + " for test " + name, e);
} }
@ -103,9 +104,9 @@ public class WalkerTest extends BaseTest {
for (int i = 0; i < resultFiles.size(); i++) { for (int i = 0; i < resultFiles.size(); i++) {
MD5DB.MD5Match result = assertMatchingMD5(name, resultFiles.get(i), expectedMD5s.get(i)); MD5DB.MD5Match result = assertMatchingMD5(name, resultFiles.get(i), expectedMD5s.get(i));
validateOutputBCFIfPossible(name, resultFiles.get(i));
if ( ! result.failed ) { if ( ! result.failed ) {
validateOutputIndex(name, resultFiles.get(i)); validateOutputIndex(name, resultFiles.get(i));
validateOutputBCFIfPossible(name, resultFiles.get(i));
md5s.add(result.expectedMD5); md5s.add(result.expectedMD5);
} else { } else {
fails.add(result); fails.add(result);
@ -337,8 +338,9 @@ public class WalkerTest extends BaseTest {
boolean gotAnException = false; boolean gotAnException = false;
try { try {
final String now = new SimpleDateFormat("HH:mm:ss").format(new Date()); final String now = new SimpleDateFormat("HH:mm:ss").format(new Date());
System.out.println(String.format("[%s] Executing test %s with GATK arguments: %s", final String cmdline = Utils.join(" ",command);
now, name, Utils.join(" ",command))); System.out.println(String.format("[%s] Executing test %s with GATK arguments: %s", now, name, cmdline));
BaseTest.log(cmdline); // also write the command line to the HTML log for convenient follow-up
CommandLineExecutable.start(instance, command); CommandLineExecutable.start(instance, command);
} catch (Exception e) { } catch (Exception e) {
gotAnException = true; gotAnException = true;

9
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
View File

@ -534,6 +534,13 @@ public class VariantContextTestProvider {
public static void assertEquals(final VCFHeader actual, final VCFHeader expected) { public static void assertEquals(final VCFHeader actual, final VCFHeader expected) {
Assert.assertEquals(actual.getMetaData().size(), expected.getMetaData().size()); Assert.assertEquals(actual.getMetaData().size(), expected.getMetaData().size());
Assert.assertEquals(actual.getMetaData(), expected.getMetaData());
// for some reason set.equals() is returning false but all paired elements are .equals(). Perhaps compare to is busted?
//Assert.assertEquals(actual.getMetaData(), expected.getMetaData());
final List<VCFHeaderLine> actualLines = new ArrayList<VCFHeaderLine>(actual.getMetaData());
final List<VCFHeaderLine> expectedLines = new ArrayList<VCFHeaderLine>(expected.getMetaData());
for ( int i = 0; i < actualLines.size(); i++ ) {
Assert.assertEquals(actualLines.get(i), expectedLines.get(i));
}
} }
} }