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Minor: cleaner way of turning off index-on-the-fly checking in case we want to turn it back on.

This commit is contained in:
Eric Banks 2012-03-18 00:53:29 -04:00
parent 344a938a70
commit 5c5d8e7cd3
1 changed files with 6 additions and 2 deletions
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8
public/java/test/org/broadinstitute/sting/WalkerTest.java
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@ -47,6 +47,7 @@ import java.util.*;
public class WalkerTest extends BaseTest { public class WalkerTest extends BaseTest {
private static final boolean ENABLE_PHONE_HOME_FOR_TESTS = false; private static final boolean ENABLE_PHONE_HOME_FOR_TESTS = false;
private static final boolean ENABLE_ON_THE_FLY_CHECK_FOR_VCF_INDEX = false;
@BeforeMethod @BeforeMethod
public void initializeRandomGenerator() { public void initializeRandomGenerator() {
@ -58,6 +59,9 @@ public class WalkerTest extends BaseTest {
} }
public void maybeValidateSupplementaryFile(final String name, final File resultFile) { public void maybeValidateSupplementaryFile(final String name, final File resultFile) {
if ( !ENABLE_ON_THE_FLY_CHECK_FOR_VCF_INDEX )
return;
File indexFile = Tribble.indexFile(resultFile); File indexFile = Tribble.indexFile(resultFile);
//System.out.println("Putative index file is " + indexFile); //System.out.println("Putative index file is " + indexFile);
if ( indexFile.exists() ) { if ( indexFile.exists() ) {
@ -75,13 +79,13 @@ 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);
Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec()); Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec());
Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath()); Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
/* tmp disable
if ( ! indexFromOutputFile.equalsIgnoreProperties(dynamicIndex) ) { if ( ! indexFromOutputFile.equalsIgnoreProperties(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", 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(), indexFromOutputFile.getProperties(),
dynamicIndex.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>();