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Bug fix for type checking RodBindings 

Now compares the feature class not the codec class.
UnitTests improvements
integrationtests on their way to actually running
This commit is contained in:
Mark DePristo 2011-08-02 22:25:41 -04:00
parent b5e843f8f0
commit 2874835997
19 changed files with 62 additions and 50 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
View File

@ -142,6 +142,10 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
return getAvailableTrackNamesAndTypes().get(fileDescriptor.getType().toUpperCase());
}
public Class getFeatureClass(RMDTriplet fileDescriptor) {
return getAvailableTrackNamesAndRecordTypes().get(fileDescriptor.getType().toUpperCase());
}
/**
* create a RMDTrack of the specified type
*

2
public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
View File

@ -70,7 +70,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
@Argument(fullName="showIndelPileups",shortName="show_indels",doc="In addition to base pileups, generate pileups of extended indel events")
public boolean SHOW_INDEL_PILEUPS = false;
@Argument(fullName="rodBind",shortName="-B",doc="Add these ROD bindings to the output Pileup", required=false)
@Argument(fullName="metadata",shortName="metadata",doc="Add these ROD bindings to the output Pileup", required=false)
public List<RodBinding<Feature>> rods;
public void initialize() {

15
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
View File

@ -25,9 +25,7 @@
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Hidden;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -49,11 +47,13 @@ import java.util.*;
/**
* Annotates variant calls with context information. Users can specify which of the available annotations to use.
*/
@Requires(value={},referenceMetaData=@RMD(name="variant",type=VariantContext.class))
@Requires(value={})
@Allows(value={DataSource.READS, DataSource.REFERENCE})
@Reference(window=@Window(start=-50,stop=50))
@By(DataSource.REFERENCE)
public class VariantAnnotator extends RodWalker<Integer, Integer> {
@Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
public RodBinding<VariantContext> variants;
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null;
@ -118,8 +118,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
listAnnotationsAndExit();
// get the list of all sample names from the variant VCF input rod, if applicable
Set<String> rodName = new HashSet<String>();
rodName.add("variant");
List<String> rodName = Arrays.asList(variants.getName());
Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), rodName);
// add the non-VCF sample from the command-line, if applicable
@ -143,7 +142,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
// note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(engine.getVCFAnnotationDescriptions());
for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList("variant")) ) {
for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())) ) {
if ( isUniqueHeaderLine(line, hInfo) )
hInfo.add(line);
}
@ -202,7 +201,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
if ( tracker == null )
return 0;
Collection<VariantContext> VCs = tracker.getValues(VariantContext.class, "variant", context.getLocation());
Collection<VariantContext> VCs = tracker.getValues(variants, context.getLocation());
if ( VCs.size() == 0 )
return 0;

5
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
View File

@ -34,7 +34,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -107,7 +106,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
for( final ReferenceOrderedDataSource source : dataSources ) {
if (source.getName().equals(comp.getVariableName())) {
if (source.getName().equals(comp.getName())) {
hInfo.add(new VCFInfoHeaderLine("ACH", 1, VCFHeaderLineType.Integer, "Allele Count from Comparison ROD at this site"));
hInfo.add(new VCFInfoHeaderLine("ANH", 1, VCFHeaderLineType.Integer, "Allele Frequency from Comparison ROD at this site"));
hInfo.add(new VCFInfoHeaderLine("AFH", 1, VCFHeaderLineType.Float, "Allele Number from Comparison ROD at this site"));
@ -116,7 +115,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
}
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getVariableName()));
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader);

5
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
View File

@ -30,7 +30,6 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibrationCurve;
@ -99,7 +98,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
public void initialize() {
samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getVariableName()));
samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
beagleWriter.print("marker alleleA alleleB");
for ( String sample : samples )
@ -303,7 +302,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
}
private void initializeVcfWriter() {
final List<String> inputNames = Arrays.asList(validation.getVariableName());
final List<String> inputNames = Arrays.asList(validation.getName());
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();

3
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphasedWalker.java
View File

@ -32,7 +32,6 @@ import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -78,7 +77,7 @@ public class VariantsToBeagleUnphasedWalker extends RodWalker<Integer, Integer>
private int testSetSize = 0;
public void initialize() {
samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getVariableName()));
samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
beagleWriter.print("I marker alleleA alleleB");
for ( String sample : samples )

6
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
View File

@ -35,8 +35,6 @@ import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Collection;
/**
* Generates an alternative reference sequence over the specified interval. Given variant ROD tracks,
@ -48,7 +46,7 @@ import java.util.Collection;
@Requires(value={DataSource.REFERENCE})
public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
@Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)
public RodBinding<VariantContext> snpmask;
public RodBinding<VariantContext> snpmask = RodBinding.makeUnbound(VariantContext.class);
private int deletionBasesRemaining = 0;
@ -63,7 +61,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
// Check to see if we have a called snp
for ( VariantContext vc : tracker.getValues(VariantContext.class) ) {
if ( ! vc.getSource().equals(snpmask.getVariableName())) {
if ( ! vc.getSource().equals(snpmask.getName())) {
if ( vc.isDeletion()) {
deletionBasesRemaining = vc.getReference().length();
// delete the next n bases, not this one

2
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
View File

@ -98,7 +98,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
private void initializeVcfWriter() {
final List<String> inputNames = Arrays.asList(variants.getVariableName());
final List<String> inputNames = Arrays.asList(variants.getName());
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();

6
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
View File

@ -59,10 +59,10 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
private long failedLocs = 0, totalLocs = 0;
public void initialize() {
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getVariableName()));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getVariableName()));
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(variants.getVariableName()) ? vcfHeaders.get(variants.getVariableName()).getMetaData() : null, samples);
final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(variants.getName()) ? vcfHeaders.get(variants.getName()).getMetaData() : null, samples);
writer.writeHeader(vcfHeader);
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
View File

@ -59,10 +59,10 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
private SortingVCFWriter writer;
public void initialize() {
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getVariableName()));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getVariableName()));
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
Set<VCFHeaderLine> headerLines = vcfHeaders.get(variants.getVariableName()).getMetaData();
Set<VCFHeaderLine> headerLines = vcfHeaders.get(variants.getName()).getMetaData();
baseWriter.writeHeader(new VCFHeader(headerLines, samples));
writer = new SortingVCFWriter(baseWriter, 200);

9
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
View File

@ -36,7 +36,6 @@ import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
@ -89,12 +88,12 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
throw new UserException.BadInput("the chain file you are using is not compatible with the reference you are trying to lift over to; please use the appropriate chain file for the given reference");
}
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getVariableName()));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getVariableName()));
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(variants.getName()));
Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
if ( vcfHeaders.containsKey(variants.getVariableName()) )
metaData.addAll(vcfHeaders.get(variants.getVariableName()).getMetaData());
if ( vcfHeaders.containsKey(variants.getName()) )
metaData.addAll(vcfHeaders.get(variants.getName()).getMetaData());
if ( RECORD_ORIGINAL_LOCATION ) {
metaData.add(new VCFInfoHeaderLine("OriginalChr", 1, VCFHeaderLineType.String, "Original contig name for the record"));
metaData.add(new VCFInfoHeaderLine("OriginalStart", 1, VCFHeaderLineType.Integer, "Original start position for the record"));

3
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
View File

@ -32,7 +32,6 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
@ -73,7 +72,7 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
iFraction = (int)(fraction * 1000.0);
// setup the header info
final List<String> inputNames = Arrays.asList(variants.getVariableName());
final List<String> inputNames = Arrays.asList(variants.getName());
Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames);
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));

7
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -35,7 +35,6 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
@ -176,7 +175,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
*/
public void initialize() {
// Get list of samples to include in the output
List<String> rodNames = Arrays.asList(variants.getVariableName());
List<String> rodNames = Arrays.asList(variants.getName());
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
@ -219,10 +218,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
// Look at the parameters to decide which analysis to perform
DISCORDANCE_ONLY = discordanceTrack.isBound();
if (DISCORDANCE_ONLY) logger.info("Selecting only variants discordant with the track: " + discordanceTrack.getVariableName());
if (DISCORDANCE_ONLY) logger.info("Selecting only variants discordant with the track: " + discordanceTrack.getName());
CONCORDANCE_ONLY = concordanceTrack.isBound();
if (CONCORDANCE_ONLY) logger.info("Selecting only variants concordant with the track: " + concordanceTrack.getVariableName());
if (CONCORDANCE_ONLY) logger.info("Selecting only variants concordant with the track: " + concordanceTrack.getName());
if (MENDELIAN_VIOLATIONS) {
if ( FAMILY_STRUCTURE_FILE != null) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableNewRodStyle.java → public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/TestRodBindings.java
View File

@ -42,7 +42,7 @@ import java.util.*;
/**
* Emits specific fields as dictated by the user from one or more VCF files.
*/
public class VariantsToTableNewRodStyle extends RodWalker<Integer, Integer> {
public class TestRodBindings extends RodWalker<Integer, Integer> {
@Output(doc="File to which results should be written",required=true)
protected PrintStream out;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
View File

@ -115,7 +115,7 @@ public class VariantValidationAssessor extends RodWalker<Pair<VariantContext, By
}
public void onTraversalDone(Integer finalReduce) {
final List<String> inputNames = Arrays.asList(variants.getVariableName());
final List<String> inputNames = Arrays.asList(variants.getName());
// setup the header fields
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();

12
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -101,8 +101,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
}
// set the appropriate sample name if necessary
if ( sampleName != null && vc.hasGenotypes() && vc.hasGenotype(variants.getVariableName()) ) {
Genotype g = Genotype.modifyName(vc.getGenotype(variants.getVariableName()), sampleName);
if ( sampleName != null && vc.hasGenotypes() && vc.hasGenotype(variants.getName()) ) {
Genotype g = Genotype.modifyName(vc.getGenotype(variants.getName()), sampleName);
Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
genotypes.put(sampleName, g);
vc = VariantContext.modifyGenotypes(vc, genotypes);
@ -117,7 +117,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
private Collection<VariantContext> getVariantContexts(RefMetaDataTracker tracker, ReferenceContext ref) {
// we need to special case the HapMap format because indels aren't handled correctly
List<Object> features = tracker.getValues(variants.getVariableName());
List<Object> features = tracker.getValues(variants.getName());
if ( features.size() > 0 && features.get(0) instanceof HapMapFeature ) {
ArrayList<VariantContext> hapmapVCs = new ArrayList<VariantContext>(features.size());
for ( Object feature : features ) {
@ -151,7 +151,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
}
refBase = ref.getBases()[hapmap.getStart() - ref.getWindow().getStart()];
}
VariantContext vc = VariantContextAdaptors.toVariantContext(variants.getVariableName(), hapmap, ref);
VariantContext vc = VariantContextAdaptors.toVariantContext(variants.getName(), hapmap, ref);
if ( vc != null ) {
if ( refBase != null ) {
Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
@ -219,10 +219,10 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
samples.add(sampleName);
} else {
// try VCF first
samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getVariableName()));
samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(variants.getName()));
if ( samples.isEmpty() ) {
List<Object> rods = tracker.getValues(variants.getVariableName());
List<Object> rods = tracker.getValues(variants.getName());
if ( rods.size() == 0 )
throw new IllegalStateException("No rod data is present");

2
public/java/src/org/broadinstitute/sting/utils/text/ListFileUtils.java
View File

@ -153,7 +153,7 @@ public class ListFileUtils {
RMDTriplet triplet = new RMDTriplet(name,type,fileName,storageType,rodBinding.getTags());
// validate triplet type
Class typeFromTribble = builderForValidation.getFeatureCodecClass(triplet);
Class typeFromTribble = builderForValidation.getFeatureClass(triplet);
if ( typeFromTribble != null && ! rodBinding.getType().isAssignableFrom(typeFromTribble) )
throw new UserException.BadArgumentValue(rodBinding.getName(),
String.format("Field %s expected type %s, but the type of the input file provided on the command line was %s",

17
public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
View File

@ -717,6 +717,23 @@ public class ParsingEngineUnitTest extends BaseTest {
Assert.assertEquals(argProvider.binding.getTags().getPositionalTags().size(), 1, "Tags aren't correctly set");
}
@Test
public void variantContextBindingArgumentTestVCF3() {
final String[] commandLine = new String[] {"-V:vcf3","foo.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(), "foo.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");
}
private class ListRodBindingArgProvider {
@Input(shortName="V", required=false)
public List<RodBinding<Feature>> bindings;

4
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -42,7 +42,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variant:VCF " + b37hapmapGenotypes + " -disc:VCF " + testFile + " -o %s -NO_HEADER",
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 --variants:VCF " + b37hapmapGenotypes + " -disc:VCF " + testFile + " -o %s -NO_HEADER",
1,
Arrays.asList("78e6842325f1f1bc9ab30d5e7737ee6e")
);
@ -55,7 +55,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
String testFile = validationDataLocation + "NA12878.hg19.example1.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc:VCF " + b37hapmapGenotypes + " --variant:VCF " + testFile + " -o %s -NO_HEADER",
"-T SelectVariants -R " + hg19Reference + " -sn NA12878 -L 20:1012700-1020000 -conc:VCF " + b37hapmapGenotypes + " --variants:VCF " + testFile + " -o %s -NO_HEADER",
1,
Arrays.asList("d2ba3ea30a810f6f0fbfb1b643292b6a")
);