zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

WalkerTest infrastructure to generate and test shadowBCF file for every generated VCF file 

-- Currently disabled
This commit is contained in:
Mark DePristo 2012-05-21 16:38:58 -04:00
parent f77d2e6965
commit cb13f16e90
1 changed files with 36 additions and 21 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

57
public/java/test/org/broadinstitute/sting/WalkerTest.java
View File

@ -38,13 +38,16 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.VariantContextTestProvider;
import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
import java.io.File;
import java.io.IOException;
import java.util.*;
public class WalkerTest extends BaseTest {
private static final boolean GENERATE_SHADOW_BCF = false;
private static final boolean ENABLE_PHONE_HOME_FOR_TESTS = false;
private static final boolean ENABLE_ON_THE_FLY_CHECK_FOR_VCF_INDEX = false;
@ -57,7 +60,19 @@ public class WalkerTest extends BaseTest {
return MD5DB.assertMatchingMD5(name, resultsFile, expectedMD5, parameterize());
}
public void maybeValidateSupplementaryFile(final String name, final File resultFile) {
public void validateOutputBCFIfPossible(final String name, final File resultFile) {
final File bcfFile = new File(resultFile.getAbsolutePath() + ".bcf");
if ( bcfFile.exists() ) {
logger.warn("Checking shadow BCF output file " + bcfFile + " against VCF file " + resultFile);
try {
VariantContextTestProvider.assertVCFandBCFFilesAreTheSame(resultFile, bcfFile);
} catch ( Exception e ) {
Assert.fail("Exception received reading shadow BCFFile " + bcfFile + " for test " + name, e);
}
}
}
public void validateOutputIndex(final String name, final File resultFile) {
if ( !ENABLE_ON_THE_FLY_CHECK_FOR_VCF_INDEX )
return;
@ -69,20 +84,15 @@ 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!");
}
assertOnDiskIndexEqualToNewlyCreatedIndex(indexFile, name, resultFile);
}
}
System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
Index indexFromOutputFile = IndexFactory.createDynamicIndex(resultFile, new VCFCodec());
Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
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.createDynamicIndex(resultFile, new VCFCodec());
Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
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",
indexFromOutputFile.getProperties(),
dynamicIndex.getProperties()));
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",
indexFromOutputFile.getProperties(),
dynamicIndex.getProperties()));
}
}
}
@ -93,7 +103,8 @@ public class WalkerTest extends BaseTest {
for (int i = 0; i < resultFiles.size(); i++) {
MD5DB.MD5Match result = assertMatchingMD5(name, resultFiles.get(i), expectedMD5s.get(i));
if ( ! result.failed ) {
maybeValidateSupplementaryFile(name, resultFiles.get(i));
validateOutputIndex(name, resultFiles.get(i));
validateOutputBCFIfPossible(name, resultFiles.get(i));
md5s.add(result.md5);
} else {
fails.add(result);
@ -125,13 +136,8 @@ public class WalkerTest extends BaseTest {
}
public class WalkerTestSpec {
// Arguments implicitly included in all Walker command lines, unless explicitly
// disabled using the disableImplicitArgs() method below.
final String IMPLICIT_ARGS = ENABLE_PHONE_HOME_FOR_TESTS ?
String.format("-et %s", GATKRunReport.PhoneHomeOption.STANDARD) :
String.format("-et %s -K %s", GATKRunReport.PhoneHomeOption.NO_ET, gatkKeyFile);
String args = "";
int nOutputFiles = -1;
List<String> md5s = null;
@ -172,7 +178,16 @@ public class WalkerTest extends BaseTest {
}
public String getArgsWithImplicitArgs() {
return args + (includeImplicitArgs ? " " + IMPLICIT_ARGS : "");
String args = this.args;
if ( includeImplicitArgs ) {
args = args + (ENABLE_PHONE_HOME_FOR_TESTS ?
String.format(" -et %s ", GATKRunReport.PhoneHomeOption.STANDARD) :
String.format(" -et %s -K %s ", GATKRunReport.PhoneHomeOption.NO_ET, gatkKeyFile));
if ( GENERATE_SHADOW_BCF )
args = args + " --generateShadowBCF ";
}
return args;
}
public void setOutputFileLocation(File outputFileLocation) {