private BCF2FieldWriter.GenotypesWriter createGenotypesWriter(final VCFHeader header, final VCFFormatHeaderLine line, final BCF2Encoder encoder, final Map<String, Integer> dict) { final String field = line.getID(); final BCF2FieldEncoder fieldEncoder = createFieldEncoder(line, encoder, dict, true); if ( field.equals(VCFConstants.GENOTYPE_KEY) ) { return new BCF2FieldWriter.GTWriter(header, fieldEncoder); } else if ( line.getID().equals(VCFConstants.GENOTYPE_FILTER_KEY) ) { return new BCF2FieldWriter.FTGenotypesWriter(header, fieldEncoder); } else if ( intGenotypeFieldAccessors.getAccessor(field) != null ) { return new BCF2FieldWriter.IGFGenotypesWriter(header, fieldEncoder, intGenotypeFieldAccessors.getAccessor(field)); } else if ( line.getType() == VCFHeaderLineType.Integer ) { return new BCF2FieldWriter.IntegerTypeGenotypesWriter(header, fieldEncoder); } else { return new BCF2FieldWriter.StaticallyTypeGenotypesWriter(header, fieldEncoder); } }
private BCF2FieldWriter.GenotypesWriter createGenotypesWriter(final VCFHeader header, final VCFFormatHeaderLine line, final BCF2Encoder encoder, final Map<String, Integer> dict) { final String field = line.getID(); final BCF2FieldEncoder fieldEncoder = createFieldEncoder(line, encoder, dict, true); if ( field.equals(VCFConstants.GENOTYPE_KEY) ) { return new BCF2FieldWriter.GTWriter(header, fieldEncoder); } else if ( line.getID().equals(VCFConstants.GENOTYPE_FILTER_KEY) ) { return new BCF2FieldWriter.FTGenotypesWriter(header, fieldEncoder); } else if ( intGenotypeFieldAccessors.getAccessor(field) != null ) { return new BCF2FieldWriter.IGFGenotypesWriter(header, fieldEncoder, intGenotypeFieldAccessors.getAccessor(field)); } else if ( line.getType() == VCFHeaderLineType.Integer ) { return new BCF2FieldWriter.IntegerTypeGenotypesWriter(header, fieldEncoder); } else { return new BCF2FieldWriter.StaticallyTypeGenotypesWriter(header, fieldEncoder); } }
private BCF2FieldWriter.GenotypesWriter createGenotypesWriter(final VCFHeader header, final VCFFormatHeaderLine line, final BCF2Encoder encoder, final Map<String, Integer> dict) { final String field = line.getID(); final BCF2FieldEncoder fieldEncoder = createFieldEncoder(line, encoder, dict, true); if ( field.equals(VCFConstants.GENOTYPE_KEY) ) { return new BCF2FieldWriter.GTWriter(header, fieldEncoder); } else if ( line.getID().equals(VCFConstants.GENOTYPE_FILTER_KEY) ) { return new BCF2FieldWriter.FTGenotypesWriter(header, fieldEncoder); } else if ( intGenotypeFieldAccessors.getAccessor(field) != null ) { return new BCF2FieldWriter.IGFGenotypesWriter(header, fieldEncoder, intGenotypeFieldAccessors.getAccessor(field)); } else if ( line.getType() == VCFHeaderLineType.Integer ) { return new BCF2FieldWriter.IntegerTypeGenotypesWriter(header, fieldEncoder); } else { return new BCF2FieldWriter.StaticallyTypeGenotypesWriter(header, fieldEncoder); } }
public void addGenotype(final BCF2Encoder encoder, final VariantContext vc, final Genotype g) throws IOException { final String fieldValue = g.getFilters(); getFieldEncoder().encodeValue(encoder, fieldValue, encodingType, nValuesPerGenotype); }
@Override protected int numElements(final VariantContext vc, final Genotype g) { return getFieldEncoder().numElements(vc, g.getFilters()); } }
@Override protected int numElements(final VariantContext vc, final Genotype g) { return getFieldEncoder().numElements(vc, g.getFilters()); } }
@Override public void addGenotype(final BCF2Encoder encoder, final VariantContext vc, final Genotype g) throws IOException { final String fieldValue = g.getFilters(); getFieldEncoder().encodeValue(encoder, fieldValue, encodingType, nValuesPerGenotype); }
@Override protected int numElements(final VariantContext vc, final Genotype g) { return getFieldEncoder().numElements(vc, g.getFilters()); } }
@Override public void addGenotype(final BCF2Encoder encoder, final VariantContext vc, final Genotype g) throws IOException { final String fieldValue = g.getFilters(); getFieldEncoder().encodeValue(encoder, fieldValue, encodingType, nValuesPerGenotype); }