Examples of RawHapMapFeature

        @Override        
        public VariantContext convert(String name, Object input, ReferenceContext ref) {
            if ( ref == null )
                throw new UnsupportedOperationException("Conversion from HapMap to VariantContext requires a reference context");


            RawHapMapFeature hapmap = (RawHapMapFeature)input;


            int index = hapmap.getStart() - ref.getWindow().getStart();
            if ( index < 0 )
                return null; // we weren't given enough reference context to create the VariantContext


            HashSet<Allele> alleles = new HashSet<Allele>();
            Allele refSNPAllele = Allele.create(ref.getBase(), true);
            int deletionLength = -1;


            Map<String, Allele> alleleMap = hapmap.getActualAlleles();
            // use the actual alleles, if available
            if ( alleleMap != null ) {
                alleles.addAll(alleleMap.values());
                Allele deletionAllele = alleleMap.get(RawHapMapFeature.INSERTION);  // yes, use insertion here (since we want the reference bases)
                if ( deletionAllele != null && deletionAllele.isReference() )
                    deletionLength = deletionAllele.length();
            } else {
                // add the reference allele for SNPs
                alleles.add(refSNPAllele);
            }


            // make a mapping from sample to genotype
            String[] samples = hapmap.getSampleIDs();
            String[] genotypeStrings = hapmap.getGenotypes();


            GenotypesContext genotypes = GenotypesContext.create(samples.length);
            for ( int i = 0; i < samples.length; i++ ) {
                // ignore bad genotypes
                if ( genotypeStrings[i].contains("N") )
                    continue;


                String a1 = genotypeStrings[i].substring(0,1);
                String a2 = genotypeStrings[i].substring(1);
                ArrayList<Allele> myAlleles = new ArrayList<Allele>(2);


                // use the mapping to actual alleles, if available
                if ( alleleMap != null ) {
                    myAlleles.add(alleleMap.get(a1));
                    myAlleles.add(alleleMap.get(a2));
                } else {
                    // ignore indels (which we can't handle without knowing the alleles)
                    if ( genotypeStrings[i].contains("I") || genotypeStrings[i].contains("D") )
                        continue;


                    Allele allele1 = Allele.create(a1, refSNPAllele.basesMatch(a1));
                    Allele allele2 = Allele.create(a2, refSNPAllele.basesMatch(a2));


                    myAlleles.add(allele1);
                    myAlleles.add(allele2);
                    alleles.add(allele1);
                    alleles.add(allele2);
                }


                Genotype g = GenotypeBuilder.create(samples[i], myAlleles);
                genotypes.add(g);
            }


            long end = hapmap.getEnd();
            if ( deletionLength > 0 )
                end += (deletionLength - 1);
            VariantContext vc = new VariantContextBuilder(name, hapmap.getChr(), hapmap.getStart(), end, alleles).id(hapmap.getName()).genotypes(genotypes).make();
            return vc;
       }

            if ( VariantContextAdaptors.canBeConvertedToVariantContext(record) ) {
                // we need to special case the HapMap format because indels aren't handled correctly
                if ( record instanceof RawHapMapFeature) {


                    // is it an indel?
                    RawHapMapFeature hapmap = (RawHapMapFeature)record;
                    if ( hapmap.getAlleles()[0].equals(RawHapMapFeature.NULL_ALLELE_STRING) || hapmap.getAlleles()[1].equals(RawHapMapFeature.NULL_ALLELE_STRING) ) {
                        // get the dbsnp object corresponding to this record (needed to help us distinguish between insertions and deletions)
                        VariantContext dbsnpVC = getDbsnp(hapmap.getName());
                        if ( dbsnpVC == null || dbsnpVC.isMixed() )
                            continue;


                        Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
                        alleleMap.put(RawHapMapFeature.DELETION, Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion()));
                        alleleMap.put(RawHapMapFeature.INSERTION, Allele.create((char)ref.getBase() + ((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
                        hapmap.setActualAlleles(alleleMap);


                        // also, use the correct positioning for insertions
                        hapmap.updatePosition(dbsnpVC.getStart());


                        if ( hapmap.getStart() < ref.getWindow().getStart() ) {
                            logger.warn("Hapmap record at " + ref.getLocus() + " represents an indel too large to be converted; skipping...");
                            continue;
                        }
                    }
                }

Examples of RawHapMapFeature

Examples of org.broadinstitute.gatk.utils.codecs.hapmap.RawHapMapFeature

Examples of org.broadinstitute.gatk.utils.codecs.hapmap.RawHapMapFeature