/** * attempt to close the VCF file; we need to flush the queue first */ @Override public void close() { stopWaitingToSort(); if (takeOwnershipOfInner) innerWriter.close(); }
public StaticallyTypeGenotypesWriter(final VCFHeader header, final BCF2FieldEncoder fieldEncoder) { super(header, fieldEncoder); encodingType = getFieldEncoder().getStaticType(); } }
private BCF2FieldWriter.SiteWriter createInfoWriter(final VCFHeader header, final VCFInfoHeaderLine line, final BCF2Encoder encoder, final Map<String, Integer> dict) { return new BCF2FieldWriter.GenericSiteWriter(header, createFieldEncoder(line, encoder, dict, false)); }
public IntGenotypeFieldAccessors() { intGenotypeFieldEncoders.put(VCFConstants.DEPTH_KEY, new IntGenotypeFieldAccessors.DPAccessor()); intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, new IntGenotypeFieldAccessors.ADAccessor()); intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_PL_KEY, new IntGenotypeFieldAccessors.PLAccessor()); intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_QUALITY_KEY, new IntGenotypeFieldAccessors.GQAccessor()); }
@Override public void addGenotype(final BCF2Encoder encoder, final VariantContext vc, final Genotype g) throws IOException { getFieldEncoder().encodeValue(encoder, ige.getValues(g), encodingType, nValuesPerGenotype); }
protected GenotypesWriter(final VCFHeader header, final BCF2FieldEncoder fieldEncoder) { super(header, fieldEncoder); if ( fieldEncoder.hasConstantNumElements() ) { nValuesPerGenotype = getFieldEncoder().numElements(); } }
@Override public void encodeValue(final BCF2Encoder encoder, final Object value, final BCF2Type type, final int minValues) throws IOException { encoder.encodeRawBytes(1, getStaticType()); } }
/** * attempt to close the VCF file; we need to flush the queue first */ @Override public void close() { stopWaitingToSort(); if (takeOwnershipOfInner) innerWriter.close(); }
public IntGenotypeFieldAccessors() { intGenotypeFieldEncoders.put(VCFConstants.DEPTH_KEY, new IntGenotypeFieldAccessors.DPAccessor()); intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, new IntGenotypeFieldAccessors.ADAccessor()); intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_PL_KEY, new IntGenotypeFieldAccessors.PLAccessor()); intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_QUALITY_KEY, new IntGenotypeFieldAccessors.GQAccessor()); }
@Override public void addGenotype(final BCF2Encoder encoder, final VariantContext vc, final Genotype g) throws IOException { getFieldEncoder().encodeValue(encoder, ige.getValues(g), encodingType, nValuesPerGenotype); }
protected GenotypesWriter(final VCFHeader header, final BCF2FieldEncoder fieldEncoder) { super(header, fieldEncoder); if ( fieldEncoder.hasConstantNumElements() ) { nValuesPerGenotype = getFieldEncoder().numElements(); } }
public StaticallyTypeGenotypesWriter(final VCFHeader header, final BCF2FieldEncoder fieldEncoder) { super(header, fieldEncoder); encodingType = getFieldEncoder().getStaticType(); } }
private BCF2FieldWriter.SiteWriter createInfoWriter(final VCFHeader header, final VCFInfoHeaderLine line, final BCF2Encoder encoder, final Map<String, Integer> dict) { return new BCF2FieldWriter.GenericSiteWriter(header, createFieldEncoder(line, encoder, dict, false)); }
@Override public void encodeValue(final BCF2Encoder encoder, final Object value, final BCF2Type type, final int minValues) throws IOException { encoder.encodeRawBytes(1, getStaticType()); } }
/** * attempt to close the VCF file; we need to flush the queue first */ @Override public void close() { stopWaitingToSort(); if (takeOwnershipOfInner) innerWriter.close(); }
public IntGenotypeFieldAccessors() { intGenotypeFieldEncoders.put(VCFConstants.DEPTH_KEY, new IntGenotypeFieldAccessors.DPAccessor()); intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_ALLELE_DEPTHS, new IntGenotypeFieldAccessors.ADAccessor()); intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_PL_KEY, new IntGenotypeFieldAccessors.PLAccessor()); intGenotypeFieldEncoders.put(VCFConstants.GENOTYPE_QUALITY_KEY, new IntGenotypeFieldAccessors.GQAccessor()); }
@Override public void addGenotype(final BCF2Encoder encoder, final VariantContext vc, final Genotype g) throws IOException { getFieldEncoder().encodeValue(encoder, ige.getValues(g), encodingType, nValuesPerGenotype); }
protected GenotypesWriter(final VCFHeader header, final BCF2FieldEncoder fieldEncoder) { super(header, fieldEncoder); if ( fieldEncoder.hasConstantNumElements() ) { nValuesPerGenotype = getFieldEncoder().numElements(); } }
public StaticallyTypeGenotypesWriter(final VCFHeader header, final BCF2FieldEncoder fieldEncoder) { super(header, fieldEncoder); encodingType = getFieldEncoder().getStaticType(); } }
private BCF2FieldWriter.SiteWriter createInfoWriter(final VCFHeader header, final VCFInfoHeaderLine line, final BCF2Encoder encoder, final Map<String, Integer> dict) { return new BCF2FieldWriter.GenericSiteWriter(header, createFieldEncoder(line, encoder, dict, false)); }