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A LocusWalker to print the haploid reference genome as a VCF file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4968 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2011-01-10 16:59:41 +00:00
parent 9648399630
commit 01c2091cd9
1 changed files with 108 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/variantutils/PrintReferenceVariantsWalker.java 100755
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/*
* Copyright (c) 2010, The Broad Institute
*
* 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.variantutils;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.commandline.Output;
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.*;
import org.broadinstitute.sting.gatk.walkers.phasing.WriteVCF;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import java.util.*;
/**
* At each locus in the input data set, prints the reference in VCF format.
*/
@By(DataSource.REFERENCE)
@Requires({DataSource.REFERENCE, DataSource.REFERENCE_BASES})
public class PrintReferenceVariantsWalker extends LocusWalker<Integer, Integer> {
@Output(doc = "File to which reference variants should be written", required = true)
protected VCFWriter writer = null;
private final static String REFERENCE = "REFERENCE";
private final static double REF_NEG_LOG_10_P_ERROR = 9.9;
private String REF_FILE_NAME = null;
public void initialize() {
this.REF_FILE_NAME = getToolkit().getArguments().referenceFile.getName();
initializeVcfWriter();
}
private void initializeVcfWriter() {
// setup the header fields:
Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
hInfo.add(new VCFHeaderLine("reference", REF_FILE_NAME));
Set<String> samples = new TreeSet<String>();
samples.add(REFERENCE);
writer.writeHeader(new VCFHeader(hInfo, samples));
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (ref == null)
return 0;
GenomeLoc refLoc = ref.getLocus();
Allele refAllele = Allele.create(ref.getBase(), true); // create a single-base allele
Set<Allele> alleles = new HashSet<Allele>();
alleles.add(refAllele);
Map<String, Genotype> genotypes = new HashMap<String, Genotype>();
boolean isPhased = true; // trivially true for a haploid genotype
Genotype haploidRefGt = new Genotype(REFERENCE, new LinkedList<Allele>(alleles), VCFConstants.MAX_GENOTYPE_QUAL, new HashSet<String>(), new HashMap<String, Object>(), isPhased);
genotypes.put(REFERENCE, haploidRefGt);
// Ensure that the genotype refers to alleles of length 1 (by using refLoc.getStart() as the stop position):
VariantContext vc = new VariantContext(REF_FILE_NAME, refLoc.getContig(), refLoc.getStart(), refLoc.getStart(), alleles, genotypes, REF_NEG_LOG_10_P_ERROR, new HashSet<String>(), new HashMap<String, Object>());
WriteVCF.writeVCF(vc, writer, logger);
return 1;
}
public Integer reduceInit() {
return 0;
}
public Integer reduce(Integer addIn, Integer sum) {
return sum + addIn;
}
public void onTraversalDone(Integer result) {
System.out.println("Processed " + result + " sites.");
}
}