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Bug fix for multisample calls in ApplyVariantClusterWalker 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3142 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-04-09 12:01:15 +00:00
parent 3f2455e346
commit f1b1e70612
1 changed files with 12 additions and 2 deletions
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14
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/ApplyVariantClustersWalker.java
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@ -2,8 +2,10 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.RodVCF; import org.broadinstitute.sting.gatk.refdata.RodVCF;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
@ -108,7 +110,6 @@ public class ApplyVariantClustersWalker extends RodWalker<ExpandingArrayList<Var
throw new StingException( "Variant Optimization Model is unrecognized. Implemented options are GAUSSIAN_MIXTURE_MODEL and K_NEAREST_NEIGHBORS" ); throw new StingException( "Variant Optimization Model is unrecognized. Implemented options are GAUSSIAN_MIXTURE_MODEL and K_NEAREST_NEIGHBORS" );
} }
// setup the header fields // setup the header fields
final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>(); final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit())); hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
@ -116,7 +117,16 @@ public class ApplyVariantClustersWalker extends RodWalker<ExpandingArrayList<Var
hInfo.add(new VCFHeaderLine("source", "VariantOptimizer")); hInfo.add(new VCFHeaderLine("source", "VariantOptimizer"));
vcfWriter = new VCFWriter( new File(OUTPUT_PREFIX + ".vcf") ); vcfWriter = new VCFWriter( new File(OUTPUT_PREFIX + ".vcf") );
final TreeSet<String> samples = new TreeSet<String>(); final TreeSet<String> samples = new TreeSet<String>();
SampleUtils.getUniquifiedSamplesFromRods(getToolkit(), samples, new HashMap<Pair<String, String>, String>()); List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
for ( ReferenceOrderedDataSource source : dataSources ) {
RMDTrack rod = source.getReferenceOrderedData();
if ( rod.getType().equals(RodVCF.class) ) {
VCFReader reader = new VCFReader(rod.getFile());
Set<String> vcfSamples = reader.getHeader().getGenotypeSamples();
samples.addAll(vcfSamples);
reader.close();
}
}
final VCFHeader vcfHeader = new VCFHeader(hInfo, samples); final VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
vcfWriter.writeHeader(vcfHeader); vcfWriter.writeHeader(vcfHeader);
} }