public BCF2GenotypeFieldDecoders(final VCFHeader header) { // TODO -- fill in appropriate decoders for each FORMAT field in the header genotypeFieldDecoder.put(VCFConstants.GENOTYPE_KEY, new GTDecoder()); // currently the generic decoder handles FILTER values properly, in so far as we don't tolerate multiple filter field values per genotype genotypeFieldDecoder.put(VCFConstants.GENOTYPE_FILTER_KEY, new FTDecoder()); genotypeFieldDecoder.put(VCFConstants.DEPTH_KEY, new DPDecoder()); genotypeFieldDecoder.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, new ADDecoder()); genotypeFieldDecoder.put(VCFConstants.GENOTYPE_PL_KEY, new PLDecoder()); genotypeFieldDecoder.put(VCFConstants.GENOTYPE_QUALITY_KEY, new GQDecoder()); }
public BCF2GenotypeFieldDecoders(final VCFHeader header) { // TODO -- fill in appropriate decoders for each FORMAT field in the header genotypeFieldDecoder.put(VCFConstants.GENOTYPE_KEY, new GTDecoder()); // currently the generic decoder handles FILTER values properly, in so far as we don't tolerate multiple filter field values per genotype genotypeFieldDecoder.put(VCFConstants.GENOTYPE_FILTER_KEY, new FTDecoder()); genotypeFieldDecoder.put(VCFConstants.DEPTH_KEY, new DPDecoder()); genotypeFieldDecoder.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, new ADDecoder()); genotypeFieldDecoder.put(VCFConstants.GENOTYPE_PL_KEY, new PLDecoder()); genotypeFieldDecoder.put(VCFConstants.GENOTYPE_QUALITY_KEY, new GQDecoder()); }
public BCF2GenotypeFieldDecoders(final VCFHeader header) { // TODO -- fill in appropriate decoders for each FORMAT field in the header genotypeFieldDecoder.put(VCFConstants.GENOTYPE_KEY, new GTDecoder()); // currently the generic decoder handles FILTER values properly, in so far as we don't tolerate multiple filter field values per genotype genotypeFieldDecoder.put(VCFConstants.GENOTYPE_FILTER_KEY, new FTDecoder()); genotypeFieldDecoder.put(VCFConstants.DEPTH_KEY, new DPDecoder()); genotypeFieldDecoder.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, new ADDecoder()); genotypeFieldDecoder.put(VCFConstants.GENOTYPE_PL_KEY, new PLDecoder()); genotypeFieldDecoder.put(VCFConstants.GENOTYPE_QUALITY_KEY, new GQDecoder()); }