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GATK now does dynamic type determination for VCF files 

Added UnitTests covering all of the cases.
This commit is contained in:
Mark DePristo 2011-08-08 14:45:46 -04:00
parent e36994e36b
commit 0810c42309
2 changed files with 115 additions and 8 deletions
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40
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.sting.commandline;
import org.apache.log4j.Logger;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.gatk.walkers.Multiplex;
import org.broadinstitute.sting.gatk.walkers.Multiplexer;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
@ -313,19 +314,42 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
String value = getArgumentValue( defaultDefinition, matches );
try {
String name = defaultDefinition.fullName;
String tribbleType;
String tribbleType = null;
Tags tags = getArgumentTags(matches);
// must have one or two tag values here
if ( tags.getPositionalTags().size() == 2 ) { // -X:name,type style
name = tags.getPositionalTags().get(0);
tribbleType = tags.getPositionalTags().get(1);
} else if ( tags.getPositionalTags().size() == 1 ) { // -X:type style
tribbleType = tags.getPositionalTags().get(0);
} else
throw new UserException.CommandLineException(
String.format("Unexpected number of positional tags for argument %s : %s. " +
"Rod bindings only suport -X:type and -X:name,type argument styles",
value, source.field.getName()));
} else {
if ( tags.getPositionalTags().size() == 1 ) {
// -X:type style is a type when we cannot determine the type dynamically
tribbleType = tags.getPositionalTags().get(0);
}
// try to determine the file type dynamically
FeatureManager manager = new FeatureManager();
File file = new File(value);
if ( file.canRead() && file.isFile() ) {
FeatureManager.FeatureDescriptor featureDescriptor = manager.getByFiletype(file);
if ( featureDescriptor != null ) {
tribbleType = featureDescriptor.getName();
logger.warn("Dynamically determined of " + file + " to be " + tribbleType);
if ( tags.getPositionalTags().size() == 1 ) {
// -X:type style is a name when we can determine the type dynamically
name = tags.getPositionalTags().get(0);
}
}
}
// now, if we haven't found a type
if ( tribbleType == null )
throw new UserException.CommandLineException(
String.format("Unexpected number of positional tags for argument %s : %s. " +
"Rod bindings only suport -X:type and -X:name,type argument styles",
value, source.field.getName()));
}
Constructor ctor = (makeRawTypeIfNecessary(type)).getConstructor(Class.class, String.class, String.class, String.class, Tags.class);
Class parameterType = getParameterizedTypeClass(type);
RodBinding result = (RodBinding)ctor.newInstance(parameterType, name, value, tribbleType, tags);

83
public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.commandline;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.testng.Assert;
@ -837,5 +838,87 @@ public class ParsingEngineUnitTest extends BaseTest {
Assert.assertEquals(argProvider.bindings.get(1).getName(), "foo2", "Name isn't set properly");
}
private final static String HISEQ_VCF = testDir + "HiSeq.10000.vcf";
private final static String TRANCHES_FILE = testDir + "tranches.6.txt";
@Test
public void variantContextBindingTestDynamicTyping1() {
final String[] commandLine = new String[] {"-V", HISEQ_VCF};
parsingEngine.addArgumentSource( VariantContextRodBindingArgProvider.class );
parsingEngine.parse( commandLine );
parsingEngine.validate();
VariantContextRodBindingArgProvider argProvider = new VariantContextRodBindingArgProvider();
parsingEngine.loadArgumentsIntoObject( argProvider );
Assert.assertEquals(argProvider.binding.getName(), "binding", "Name isn't set properly");
Assert.assertEquals(argProvider.binding.getSource(), HISEQ_VCF, "Source isn't set to its expected value");
Assert.assertEquals(argProvider.binding.getType(), VariantContext.class, "Type isn't set to its expected value");
Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 0, "Tags aren't correctly set");
}
@Test
public void variantContextBindingTestDynamicTypingNameAsSingleArgument() {
final String[] commandLine = new String[] {"-V:name", HISEQ_VCF};
parsingEngine.addArgumentSource( VariantContextRodBindingArgProvider.class );
parsingEngine.parse( commandLine );
parsingEngine.validate();
VariantContextRodBindingArgProvider argProvider = new VariantContextRodBindingArgProvider();
parsingEngine.loadArgumentsIntoObject( argProvider );
Assert.assertEquals(argProvider.binding.getName(), "name", "Name isn't set properly");
Assert.assertEquals(argProvider.binding.getSource(), HISEQ_VCF, "Source isn't set to its expected value");
Assert.assertEquals(argProvider.binding.getType(), VariantContext.class, "Type isn't set to its expected value");
Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");
}
@Test()
public void variantContextBindingTestDynamicTypingTwoTagsPassing() {
final String[] commandLine = new String[] {"-V:name,vcf", HISEQ_VCF};
parsingEngine.addArgumentSource( VariantContextRodBindingArgProvider.class );
parsingEngine.parse( commandLine );
parsingEngine.validate();
VariantContextRodBindingArgProvider argProvider = new VariantContextRodBindingArgProvider();
parsingEngine.loadArgumentsIntoObject( argProvider );
Assert.assertEquals(argProvider.binding.getName(), "name", "Name isn't set properly");
Assert.assertEquals(argProvider.binding.getSource(), HISEQ_VCF, "Source isn't set to its expected value");
Assert.assertEquals(argProvider.binding.getType(), VariantContext.class, "Type isn't set to its expected value");
Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 2, "Tags aren't correctly set");
}
@Test()
public void variantContextBindingTestDynamicTypingTwoTagsCausingTypeFailure() {
final String[] commandLine = new String[] {"-V:name,beagle", HISEQ_VCF};
parsingEngine.addArgumentSource( VariantContextRodBindingArgProvider.class );
parsingEngine.parse( commandLine );
parsingEngine.validate();
VariantContextRodBindingArgProvider argProvider = new VariantContextRodBindingArgProvider();
parsingEngine.loadArgumentsIntoObject(argProvider);
Assert.assertEquals(argProvider.binding.getName(), "name", "Name isn't set properly");
Assert.assertEquals(argProvider.binding.getSource(), HISEQ_VCF, "Source isn't set to its expected value");
Assert.assertEquals(argProvider.binding.getType(), VariantContext.class, "Type isn't set to its expected value");
Assert.assertEquals(argProvider.binding.getTribbleType(), "beagle", "Type isn't set to its expected value");
Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 2, "Tags aren't correctly set");
}
@Test(expectedExceptions = UserException.class)
public void variantContextBindingTestDynamicTypingUnknownTribbleType() {
final String[] commandLine = new String[] {"-V", TRANCHES_FILE};
parsingEngine.addArgumentSource( VariantContextRodBindingArgProvider.class );
parsingEngine.parse( commandLine );
parsingEngine.validate();
VariantContextRodBindingArgProvider argProvider = new VariantContextRodBindingArgProvider();
parsingEngine.loadArgumentsIntoObject( argProvider );
}
}