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Bring CombineVariants back to public since it's used for SG. I needed to break ChromosomeCountConstants out of ChromosomeCounts to make this work.

This commit is contained in:
Eric Banks 2013-01-09 10:39:48 -05:00
parent c87ad8c0ef
commit 676e79542a
3 changed files with 48 additions and 12 deletions
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12
protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
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@ -35,10 +35,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.variantcontext.VariantContextUtils;
@ -52,12 +50,6 @@ import java.util.*;
*/
public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
public static final VCFInfoHeaderLine[] descriptions = {
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY),
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY),
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) };
private Set<String> founderIds = new HashSet<String>();
public Map<String, Object> annotate(final RefMetaDataTracker tracker,
@ -78,8 +70,8 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn
}
public List<String> getKeyNames() {
return Arrays.asList(keyNames);
return Arrays.asList(ChromosomeCountConstants.keyNames);
}
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(descriptions); }
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(ChromosomeCountConstants.descriptions); }
}

44
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java 100755
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@ -0,0 +1,44 @@
/*
* Copyright (c) 2010.
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.annotator;
import org.broadinstitute.variant.vcf.VCFConstants;
import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
/**
* Keys and descriptions for the common chromosome count annotations
*/
public class ChromosomeCountConstants {
public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
public static final VCFInfoHeaderLine[] descriptions = {
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY),
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY),
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) };
}

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java → public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
View File

@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.Window;
import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCountConstants;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.vcf.*;
@ -217,7 +217,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
if ( SET_KEY != null )
headerLines.add(new VCFInfoHeaderLine(SET_KEY, 1, VCFHeaderLineType.String, "Source VCF for the merged record in CombineVariants"));
if ( !ASSUME_IDENTICAL_SAMPLES )
headerLines.addAll(Arrays.asList(ChromosomeCounts.descriptions));
headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions));
VCFHeader vcfHeader = new VCFHeader(headerLines, samples);
vcfHeader.setWriteCommandLine(!SUPPRESS_COMMAND_LINE_HEADER);
vcfWriter.writeHeader(vcfHeader);