public VCFRecordCodec(final VCFHeader header, final boolean allowMissingFieldsInHeader) { this.vcfEncoder = new VCFEncoder(header, allowMissingFieldsInHeader, false); // Explicitly set the version because it's not available in the header itself. this.vcfDecoder.setVCFHeader(header, VCFHeaderVersion.VCF4_2); }
public VCFRecordCodec(final VCFHeader header) { this.vcfEncoder = new VCFEncoder(header, false); // Explicitly set the version because it's not available in the header itself. this.vcfDecoder.setVCFHeader(header, VCFHeaderVersion.VCF4_1); }
public VCFRecordCodec(final VCFHeader header, final boolean allowMissingFieldsInHeader) { this.vcfEncoder = new VCFEncoder(header, allowMissingFieldsInHeader, false); // Explicitly set the version because it's not available in the header itself. this.vcfDecoder.setVCFHeader(header, VCFHeaderVersion.VCF4_2); }
@Override public void setHeader(final VCFHeader header) { if (outputHasBeenWritten) { throw new IllegalStateException("The header cannot be modified after the header or variants have been written to the output stream."); } this.mHeader = doNotWriteGenotypes ? new VCFHeader(header.getMetaDataInSortedOrder()) : header; this.vcfEncoder = new VCFEncoder(this.mHeader, this.allowMissingFieldsInHeader, this.writeFullFormatField); } }
@Override public void setHeader(final VCFHeader header) { if (outputHasBeenWritten) { throw new IllegalStateException("The header cannot be modified after the header or variants have been written to the output stream."); } this.mHeader = doNotWriteGenotypes ? new VCFHeader(header.getMetaDataInSortedOrder()) : header; this.vcfEncoder = new VCFEncoder(this.mHeader, this.allowMissingFieldsInHeader, this.writeFullFormatField); } }
@Override public void writeHeader(final VCFHeader header) { // note we need to update the mHeader object after this call because they header // may have genotypes trimmed out of it, if doNotWriteGenotypes is true try { this.mHeader = writeHeader(header, writer, doNotWriteGenotypes, getVersionLine(), getStreamName()); this.vcfEncoder = new VCFEncoder(this.mHeader, this.allowMissingFieldsInHeader); writeAndResetBuffer(); } catch ( IOException e ) { throw new RuntimeException("Couldn't write file " + getStreamName(), e); } }
builder.append(genotypeFormatString); final VCFEncoder encoder = new VCFEncoder(header, true, false); final Map<Allele, String> alleleStrings = encoder.buildAlleleStrings(vc); encoder.addGenotypeData(vc, alleleStrings, genotypeAttributeKeys, builder);
builder.append(genotypeFormatString); final VCFEncoder encoder = new VCFEncoder(header, true, false); final Map<Allele, String> alleleStrings = encoder.buildAlleleStrings(vc); encoder.addGenotypeData(vc, alleleStrings, genotypeAttributeKeys, builder);
builder.append(genotypeFormatString); final VCFEncoder encoder = new VCFEncoder(header, true, false); final Map<Allele, String> alleleStrings = encoder.buildAlleleStrings(vc); encoder.addGenotypeData(vc, alleleStrings, genotypeAttributeKeys, builder);
final VCFHeader header = createSyntheticHeader(Arrays.asList("Sample1")); final VCFEncoder dropMissing = new VCFEncoder(header, false, false); final VCFEncoder keepMissing = new VCFEncoder(header, false, true); final VariantContextBuilder baseVC = new VariantContextBuilder().chr("1").start(1).stop(1).noID().passFilters().log10PError(1).alleles("A", "C"); final GenotypeBuilder baseGT = new GenotypeBuilder("Sample1").alleles(Arrays.asList(Allele.NO_CALL, Allele.NO_CALL));