From 01c2091cd97a793fee78342a87ff861df35fa1a2 Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 10 Jan 2011 16:59:41 +0000
Subject: [PATCH] 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
---
 .../PrintReferenceVariantsWalker.java         | 108 ++++++++++++++++++
 1 file changed, 108 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/walkers/variantutils/PrintReferenceVariantsWalker.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/PrintReferenceVariantsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/PrintReferenceVariantsWalker.java
new file mode 100755
index 000000000..4a5af3edb
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/PrintReferenceVariantsWalker.java
@@ -0,0 +1,108 @@
+/*
+ * 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.");
+    }
+}
\ No newline at end of file