protected BCF2GenotypeFieldDecoders.Decoder getGenotypeFieldDecoder(final String field) { return gtFieldDecoders.getDecoder(field); }
@Override public void setHeader(VCFHeader header) { genoFieldDecoders = new BCF2GenotypeFieldDecoders(header); fieldDict = BCF2Utils.makeDictionary(header); builders = new GenotypeBuilder[header.getNGenotypeSamples()]; final List<String> genotypeSamples = header.getGenotypeSamples(); for (int i = 0; i < builders.length; ++i) builders[i] = new GenotypeBuilder(genotypeSamples.get(i)); sampleNamesInOrder = header.getSampleNamesInOrder(); sampleNameToOffset = header.getSampleNameToOffset(); }
@Override public void setHeader(VCFHeader header) { genoFieldDecoders = new BCF2GenotypeFieldDecoders(header); fieldDict = BCF2Utils.makeDictionary(header); builders = new GenotypeBuilder[header.getNGenotypeSamples()]; final List<String> genotypeSamples = header.getGenotypeSamples(); for (int i = 0; i < builders.length; ++i) builders[i] = new GenotypeBuilder(genotypeSamples.get(i)); sampleNamesInOrder = header.getSampleNamesInOrder(); sampleNameToOffset = header.getSampleNameToOffset(); }
@Override public void setHeader(VCFHeader header) { genoFieldDecoders = new BCF2GenotypeFieldDecoders(header); fieldDict = BCF2Utils.makeDictionary(header); builders = new GenotypeBuilder[header.getNGenotypeSamples()]; final List<String> genotypeSamples = header.getGenotypeSamples(); for (int i = 0; i < builders.length; ++i) builders[i] = new GenotypeBuilder(genotypeSamples.get(i)); sampleNamesInOrder = header.getSampleNamesInOrder(); sampleNameToOffset = header.getSampleNameToOffset(); }
protected BCF2GenotypeFieldDecoders.Decoder getGenotypeFieldDecoder(final String field) { return gtFieldDecoders.getDecoder(field); }
gtFieldDecoders = new BCF2GenotypeFieldDecoders(header);
@Requires("field != null") @Ensures("result != null") protected BCF2GenotypeFieldDecoders.Decoder getGenotypeFieldDecoder(final String field) { return gtFieldDecoders.getDecoder(field); }
gtFieldDecoders = new BCF2GenotypeFieldDecoders(header);
final int numElems = hd.decoder.decodeNumberOfElements(type); hd.getGenoFieldDecoders().getDecoder(field).decode( alleles, field, hd.decoder, type, numElems, builders);
gtFieldDecoders = new BCF2GenotypeFieldDecoders(header);
final int numElems = hd.decoder.decodeNumberOfElements(type); hd.getGenoFieldDecoders().getDecoder(field).decode( alleles, field, hd.decoder, type, numElems, builders);
final int numElems = hd.decoder.decodeNumberOfElements(type); hd.getGenoFieldDecoders().getDecoder(field).decode( alleles, field, hd.decoder, type, numElems, builders);