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First revision of command-line argument support for GenotypeWriter. Also, fixed the damn build. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2416 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-12-20 19:19:23 +00:00
parent 4ff61097cf
commit 9e53c06328
3 changed files with 148 additions and 7 deletions
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4
java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
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@ -8,6 +8,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.io.stubs.OutputStreamArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescriptor;
import org.broadinstitute.sting.gatk.io.stubs.GenotypeWriterArgumentTypeDescriptor;
import java.io.File;
import java.io.FileNotFoundException;
@ -96,7 +97,8 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
* @return A collection of type descriptors generating implementation-dependent placeholders.
*/
protected Collection<ArgumentTypeDescriptor> getArgumentTypeDescriptors() {
return Arrays.asList( new SAMFileReaderArgumentTypeDescriptor(GATKEngine),
return Arrays.asList( new GenotypeWriterArgumentTypeDescriptor(GATKEngine),
new SAMFileReaderArgumentTypeDescriptor(GATKEngine),
new SAMFileWriterArgumentTypeDescriptor(GATKEngine),
new OutputStreamArgumentTypeDescriptor(GATKEngine) );
}

139
java/src/org/broadinstitute/sting/gatk/io/stubs/GenotypeWriterArgumentTypeDescriptor.java 100644
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@ -0,0 +1,139 @@
package org.broadinstitute.sting.gatk.io.stubs;
import org.broadinstitute.sting.utils.cmdLine.ArgumentTypeDescriptor;
import org.broadinstitute.sting.utils.cmdLine.ArgumentSource;
import org.broadinstitute.sting.utils.cmdLine.ArgumentMatches;
import org.broadinstitute.sting.utils.cmdLine.ArgumentDefinition;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import java.io.File;
import java.util.List;
import java.util.Arrays;
import net.sf.samtools.SAMFileReader;
/**
* Injects new command-line arguments into the system providing support for the genotype writer.
*
* @author mhanna
* @version 0.1
*/
public class GenotypeWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
/**
* The engine into which output stubs should be fed.
*/
private GenomeAnalysisEngine engine;
/**
* Create a new GenotypeWriter argument, notifying the given engine when that argument has been created.
* @param engine
*/
public GenotypeWriterArgumentTypeDescriptor(GenomeAnalysisEngine engine) {
this.engine = engine;
}
/**
* Reports whether this ArgumentTypeDescriptor supports the given type.
* @param type The type to check.
* @return True if the argument is a GenotypeWriter.
*/
@Override
public boolean supports( Class type ) {
return GenotypeWriter.class.equals(type);
}
/**
* Create the argument definitions associated with this source.
* Assumes that this type descriptor is relevant for this source.
* @param source Source class and field for the given argument.
* @return A list of all associated argument definitions.
*/
@Override
public List<ArgumentDefinition> createArgumentDefinitions( ArgumentSource source ) {
return Arrays.asList( createGenotypeFileArgumentDefinition(source),
createGenotypeFormatArgumentDefinition(source) );
}
/**
* Convert the given argument matches into a single object suitable for feeding into the ArgumentSource.
* @param source Source for this argument.
* @param type
* @param matches Matches that match with this argument.
* @return Transform from the matches into the associated argument.
*/
@Override
public Object parse( ArgumentSource source, Class type, ArgumentMatches matches ) {
String writerFileName = getArgumentValue(createGenotypeFileArgumentDefinition(source),matches);
if(writerFileName == null)
throw new StingException("Genotype format was supplied, but no file was supplied to contain the genotype info..");
String genotypeFormatText = getArgumentValue(createGenotypeFormatArgumentDefinition(source),matches);
GenotypeWriterFactory.GENOTYPE_FORMAT genotypeFormat = GenotypeWriterFactory.GENOTYPE_FORMAT.VCF;
if(genotypeFormatText != null) {
try {
genotypeFormat = Enum.valueOf(GenotypeWriterFactory.GENOTYPE_FORMAT.class,genotypeFormatText);
}
catch(IllegalArgumentException ex) {
throw new StingException(String.format("Genotype format %s is invalid.",genotypeFormatText));
}
}
GenotypeWriterStub stub = new GenotypeWriterStub(engine, new File(writerFileName),genotypeFormat);
engine.addOutput(stub);
return stub;
}
/**
* Gets the definition of the argument representing the BAM file itself.
* @param source Argument source for the BAM file. Must not be null.
* @return Argument definition for the BAM file itself. Will not be null.
*/
private ArgumentDefinition createGenotypeFileArgumentDefinition(ArgumentSource source) {
Argument description = this.getArgumentDescription(source);
boolean isFullNameProvided = description.fullName().trim().length() > 0;
boolean isShortNameProvided = description.shortName().trim().length() > 0;
String fullName = isFullNameProvided ? description.fullName().trim() : "variants_out";
// If the short name is provided, use that. If the user hasn't provided any names at all, use
// the default. If somewhere in the middle, leave the short name blank.
String shortName;
if( isShortNameProvided )
shortName = description.shortName().trim();
else if( !isFullNameProvided )
shortName = "varout";
else
shortName = null;
return new ArgumentDefinition( source,
fullName,
shortName,
getDoc(source),
isRequired(source),
getExclusiveOf(source),
getValidationRegex(source) );
}
/**
* Creates the optional compression level argument for the BAM file.
* @param source Argument source for the BAM file. Must not be null.
* @return Argument definition for the BAM file itself. Will not be null.
*/
private ArgumentDefinition createGenotypeFormatArgumentDefinition(ArgumentSource source) {
return new ArgumentDefinition( source,
"variant_output_format",
"vf",
"Format to be used to represent variants; default is VCF",
false,
null,
null );
}
}

12
java/test/org/broadinstitute/sting/playground/gatk/walkers/ConcordanceTruthTableTest.java
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@ -73,12 +73,12 @@ public class ConcordanceTruthTableTest extends BaseTest {
List<Pair<Genotype,Genotype>> homNoRef = new ArrayList<Pair<Genotype,Genotype>>(1);
homNoRef.add(new Pair<Genotype,Genotype>(hom1,null));
Pair<Genotype,Pair<Integer,Integer>> countShouldBeOne = ctt.getPooledAlleleFrequency(oneHet,'G');
Pair<Genotype,Pair<Integer,Integer>> countShouldBeTwo = ctt.getPooledAlleleFrequency(oneHom,'G');
Pair<Genotype,Pair<Integer,Integer>> countShouldBeFour = ctt.getPooledAlleleFrequency(twoHetOneHom,'G');
Pair<Genotype,Pair<Integer,Integer>> countShouldBeSix = ctt.getPooledAlleleFrequency(twoHetTwoHom,'G');
Pair<Genotype,Pair<Integer,Integer>> countShouldBeThree = ctt.getPooledAlleleFrequency(hetHomNoRef,'G');
Pair<Genotype,Pair<Integer,Integer>> countShouldBeTwoHereToo = ctt.getPooledAlleleFrequency(homNoRef, 'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeOne = ctt.getPooledAlleleFrequency(oneHet,'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeTwo = ctt.getPooledAlleleFrequency(oneHom,'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeFour = ctt.getPooledAlleleFrequency(twoHetOneHom,'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeSix = ctt.getPooledAlleleFrequency(twoHetTwoHom,'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeThree = ctt.getPooledAlleleFrequency(hetHomNoRef,'G');
Pair<Integer,Pair<Integer,Integer>> countShouldBeTwoHereToo = ctt.getPooledAlleleFrequency(homNoRef, 'G');
int expecChips = 4+4+6+7+2+1;
int numChips = countShouldBeOne.getSecond().getSecond() + countShouldBeTwo.getSecond().getSecond() +