Converter from HapMap chip genotype data to VCF added; HapMapGenotypeROD adjusted to not convert from Hg18 to b36 formatting of contigs

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2447 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/HapMapGenotypeROD.java

@@ -16,7 +16,9 @@ public class HapMapGenotypeROD extends TabularROD
 	{
 		//System.out.printf("chrom: %s; pos: %s\n", this.get("chrom"), this.get("pos"));
        
-		return GenomeLocParser.createGenomeLoc(this.get("chrom").replaceAll("chr", ""), Long.parseLong(this.get("pos")));
+		// For converting from Hg18 to b36 format:
+        // return GenomeLocParser.createGenomeLoc(this.get("chrom").replaceAll("chr", ""), Long.parseLong(this.get("pos")));
+        return GenomeLocParser.createGenomeLoc(this.get("chrom"), Long.parseLong(this.get("pos")));
     }
 
 	public String[] getSampleIDs()

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/HapMap2VCF.java

@@ -0,0 +1,151 @@
+package org.broadinstitute.sting.playground.gatk.walkers.variantstovcf;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.HapMapGenotypeROD;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
+
+/**
+ * Converts HapMap genotype information to VCF format
+ */
+public class HapMap2VCF extends RodWalker<Integer, Integer> {
+
+    String[] sample_ids;
+
+    /**
+     * For each HapMap record, generate and print the VCF record string
+     * Output the VCF header if this is the first record
+     */
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( tracker == null )
+            return 0;
+
+        Iterator<ReferenceOrderedDatum> rods = tracker.getAllRods().iterator();
+        boolean first_hapmap_rod = true;
+        while ( rods.hasNext() ) {
+            ReferenceOrderedDatum rod = rods.next();
+            if ( rod instanceof HapMapGenotypeROD ) {
+                HapMapGenotypeROD hapmap_rod = (HapMapGenotypeROD) rod;
+                if (first_hapmap_rod) {
+                    out.println(VCFHeaderString(hapmap_rod.getSampleIDs()));
+                    first_hapmap_rod = false;
+                }
+
+                // Get reference and alternate bases
+
+                Character alt_allele, ref_allele;
+
+                Set<Character> observed_alleles = getObservedAlleles (hapmap_rod.getGenotypes());
+                if (observed_alleles.contains('N'))
+                    observed_alleles.remove('N');
+                ref_allele = ref.getBase();
+                if (observed_alleles.contains(ref_allele))
+                    observed_alleles.remove(ref_allele);
+                if (observed_alleles.isEmpty()) {
+                    alt_allele = ref_allele; // ## todo: Confirm that alt allele becomes ref allele 
+                }else{
+                    if (observed_alleles.size() != 1) {
+                        out.println("Error: more than 2 alleles found in hapmap chip position");
+                        alt_allele = 'N';
+                        System.exit(1);
+                    }else{
+                        alt_allele = observed_alleles.iterator().next();
+                    }
+                }
+
+                // Print all position specific info
+                String vcf = hapmap_rod.get("chrom")+"\t"+
+                             hapmap_rod.get("pos")+"\t"+
+                             hapmap_rod.get("rs#")+"\t"+
+                             ref_allele+"\t"+
+                             alt_allele+"\t"+
+                             "99\t0\t.\tGT:GQ";
+                out.print(vcf);
+
+                // Print each sample's genotype info
+
+                String allele_strings = "";
+                for (String genotype : hapmap_rod.getGenotypes()) {
+                    String allele_str = ""; // one allele string
+                    Integer GQ = 99;
+                    for (Character allele : genotype.toCharArray()) {
+                        if (allele == ref_allele) {
+                            allele_str += "0";
+                        }else{
+                            if (allele == alt_allele) {
+                                allele_str += "1";
+                            }else{
+                                if (allele == 'N') {
+                                    allele_str += "0";
+                                    GQ = 0;
+                                }else{
+                                    out.println("ERROR: Unexpected tri-allelic site detected");
+                                    System.exit(1);
+                                }
+                            }
+                        }
+                        if (allele_str.length() == 1) {
+                            allele_str += "/";
+                        }
+                    }
+                    allele_strings += "\t" + allele_str+":"+GQ;
+                }
+
+                out.println(allele_strings);
+            }
+        }
+
+        return 1;
+    }
+
+    public static Set<Character> getObservedAlleles (String[] genotypes) {
+        Set<Character> observed_alleles = new HashSet<Character>();
+        for (String genotype : genotypes)
+            for (Character allele : genotype.toCharArray())
+                if (!observed_alleles.contains(allele))
+                    observed_alleles.add(allele);
+
+        return observed_alleles;
+    }
+
+    public String VCFHeaderString (String[] sample_ids) {
+        String header = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT";
+        for (String sample_id : sample_ids)
+            header += "\t" + sample_id;
+
+        return header;
+    }
+
+    /**
+     * Initialize the number of loci processed to zero.
+     *
+     * @return 0
+     */
+    public Integer reduceInit() {
+        out.println("#fileformat=VCFv3.3");
+        out.println("##reference=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta");
+        out.println("##source=VariantsToVCF");
+
+        return 0;
+    }
+
+    /**
+     * Increment the number of rods processed.
+     *
+     * @param value result of the map.
+     * @param sum   accumulator for the reduce.
+     * @return the new number of rods processed.
+     */
+    public Integer reduce(Integer value, Integer sum) {
+        return sum + value;
+    }
+
+    public void onTraversalDone(Integer value) {}
+
+}