@Override public VCFRecordCodec clone() { return new VCFRecordCodec(this.vcfEncoder.getVCFHeader()); } }
@Override public VCFRecordCodec clone() { return new VCFRecordCodec(this.vcfEncoder.getVCFHeader(), this.vcfEncoder.getAllowMissingFieldsInHeader()); } }
@Override public VCFRecordCodec clone() { return new VCFRecordCodec(this.vcfEncoder.getVCFHeader(), this.vcfEncoder.getAllowMissingFieldsInHeader()); } }
SortingCollection.newInstance( VariantContext.class, new VCFRecordCodec(outputHeader, VALIDATION_STRINGENCY != ValidationStringency.STRICT), outputHeader.getVCFRecordComparator(), MAX_RECORDS_IN_RAM,
SortingCollection.newInstance( VariantContext.class, new VCFRecordCodec(outputHeader, VALIDATION_STRINGENCY != ValidationStringency.STRICT), outputHeader.getVCFRecordComparator(), MAX_RECORDS_IN_RAM,
collection = SortingCollection.newInstance( VariantContext.class, new VCFRecordCodec(header), sortComparator, processContext.getFileSystemContext().getMaxBufferedRecordsPerFile(),
new VCFRecordCodec(outHeader, ALLOW_MISSING_FIELDS_IN_HEADER || VALIDATION_STRINGENCY != ValidationStringency.STRICT), outHeader.getVCFRecordComparator(), MAX_RECORDS_IN_RAM,
new VCFRecordCodec(outHeader, ALLOW_MISSING_FIELDS_IN_HEADER || VALIDATION_STRINGENCY != ValidationStringency.STRICT), outHeader.getVCFRecordComparator(), MAX_RECORDS_IN_RAM,