CG var format is screwed up and doesn't quite fit into the VariantsToVCF mold (we need to see multiple records before we can assign genotypes to a given position), so it's safer to keep this separate from the other well-behaved formats. Hopefully, it's temporary anyways.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5216 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CGVarToVCF.java

@@ -0,0 +1,115 @@
+/*
+ * 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.Argument;
+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 java.util.*;
+
+/**
+ * Converts variants from the Complete Genomics VAR format to VCF format.
+ */
+@Requires(value={},referenceMetaData=@RMD(name=CGVarToVCF.INPUT_ROD_NAME, type=VariantContext.class))
+@Reference(window=@Window(start=-40,stop=400))
+public class CGVarToVCF extends RodWalker<Integer, Integer> {
+
+    public static final String INPUT_ROD_NAME = "variant";
+
+    @Output(doc="File to which variants should be written", required=true)
+    protected VCFWriter vcfWriter = null;
+
+    @Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod", required=true)
+    protected String sampleName = null;
+
+    public void initialize() {
+        HashSet<String> samples = new HashSet<String>(1);
+        samples.add(sampleName);
+        vcfWriter.writeHeader(new VCFHeader(new HashSet<VCFHeaderLine>(), samples));
+    }
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( tracker == null )
+            return 0;
+
+        Collection<VariantContext> contexts = tracker.getVariantContexts(ref, INPUT_ROD_NAME, null, ref.getLocus(), true, false);
+
+        // for now, we don't support the mixed type
+        if ( contexts.size() == 0 || contexts.size() > 2 )
+            return 0;
+
+        Iterator<VariantContext> iter = contexts.iterator();
+        if ( contexts.size() == 1 ) {
+            writeHet(iter.next(), ref.getBase());
+        } else {
+            VariantContext vc1 = iter.next();
+            VariantContext vc2 = iter.next();
+            if ( vc1.getType().equals(vc2.getType()) )
+                writeHom(vc1, ref.getBase());
+        }
+
+        return 0;
+    }
+
+    private void writeHet(VariantContext vc, byte ref) {
+        List<Allele> alleles = new ArrayList<Allele>(vc.getAlleles());
+        Genotype g = new Genotype(sampleName, alleles);
+        write(vc, ref, g);
+    }
+
+    private void writeHom(VariantContext vc, byte ref) {
+        List<Allele> alleles = new ArrayList<Allele>(2);
+        alleles.add(vc.getAlternateAllele(0));
+        alleles.add(vc.getAlternateAllele(0));
+        Genotype g = new Genotype(sampleName, alleles);
+        write(vc, ref, g);
+    }
+
+    private void write(VariantContext vc, byte ref, Genotype g) {
+        HashMap<String, Genotype> genotypes = new HashMap<String, Genotype>(1);
+        genotypes.put(sampleName, g);
+        vc = VariantContext.modifyGenotypes(vc, genotypes);
+        if ( vc.isSNP() )
+            vc = VariantContext.modifyLocation(vc, vc.getChr(), vc.getStart()+1, vc.getStart()+1);        
+        vcfWriter.add(vc, ref);
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce(Integer value, Integer sum) {
+        return value + sum;
+    }
+}