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Removing more references to VCFRecord 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3790 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-14 16:34:15 +00:00
parent af23762778
commit 78a4d8ec3d
2 changed files with 2 additions and 27 deletions
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16
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
View File

@ -29,15 +29,12 @@ import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
import org.broadinstitute.sting.utils.text.XReadLines;
@ -106,17 +103,8 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
hInfo.add(new VCFHeaderLine("source", "VariantOptimizer"));
vcfWriter = new VCFWriter( new File(OUTPUT_FILENAME) );
final TreeSet<String> samples = new TreeSet<String>();
final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
for( final ReferenceOrderedDataSource source : dataSources ) {
final RMDTrack rod = source.getReferenceOrderedData();
if( rod.getRecordType().equals(VCFRecord.class) ) {
final VCFReader reader = new VCFReader(rod.getFile());
final Set<String> vcfSamples = reader.getHeader().getGenotypeSamples();
samples.addAll(vcfSamples);
reader.close();
}
}
samples.addAll(SampleUtils.getSampleListWithVCFHeader(getToolkit(), null));
for( int iii = 1; iii < filterName.size(); iii++ ) {
hInfo.add(new VCFFilterHeaderLine(filterName.get(iii), String.format("FDR tranche level at qual " + qCuts.get(iii))));
}

13
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
View File

@ -45,19 +45,6 @@ public class VCFUtils {
*/
private VCFUtils() { }
public static Set<RMDTrack> getRodVCFs(GenomeAnalysisEngine toolkit) {
Set<RMDTrack> vcfs = new HashSet<RMDTrack>();
for ( ReferenceOrderedDataSource source : toolkit.getRodDataSources() ) {
RMDTrack rod = source.getReferenceOrderedData();
if ( rod.getRecordType().equals(VCFRecord.class) ) {
vcfs.add(rod);
}
}
return vcfs;
}
/**
* Gets the header fields from all VCF rods input by the user
*