variant_header_builder.h

Go to the documentation of this file.

#ifndef gamgee__variant_header_builder__guard
#define gamgee__variant_header_builder__guard

#include "variant_header.h"
#include "variant_reader.h"

#include "../utils/utils.h"
#include "../utils/hts_memory.h"

#include "htslib/vcf.h"

#include <memory>

namespace gamgee {

class VariantHeaderBuilder {
 public: 

  VariantHeaderBuilder() noexcept;
  VariantHeaderBuilder(const VariantHeader& header);
  // TODO: version with move semantics

  VariantHeaderBuilder(const VariantHeaderBuilder& other) = delete;
  VariantHeaderBuilder& operator=(const VariantHeaderBuilder& other) = delete;

  VariantHeaderBuilder(VariantHeaderBuilder&& other) = default;
  VariantHeaderBuilder& operator=(VariantHeaderBuilder&& other) = default;

  VariantHeaderBuilder& add_chromosome(const std::string& id, const std::string& length = "", const std::string& url = "", const std::string& extra = "");
  VariantHeaderBuilder& add_filter(const std::string& id, const std::string& description = "", const std::string& extra = "");
  VariantHeaderBuilder& add_shared_field(const std::string& id, const std::string& number, const std::string& type, const std::string& description = "", const std::string& source = "", const std::string& version = "", const std::string& extra = "");
  VariantHeaderBuilder& add_individual_field(const std::string& id, const std::string& number, const std::string& type, const std::string& description = "", const std::string& extra = "");
  VariantHeaderBuilder& add_sample(const std::string& sample);
  VariantHeaderBuilder& add_source(const std::string& source);

  VariantHeaderBuilder& advanced_add_arbitrary_line(const std::string& line);

  VariantHeaderBuilder& merge(const VariantHeader& other_header);

  VariantHeader build() const {
    // Need to sync the header before returning it so that changes will be reflected in the final product
    bcf_hdr_sync(m_header.get());
    return VariantHeader{utils::make_shared_variant_header(utils::variant_header_deep_copy(m_header.get()))};
  }

  VariantHeader one_time_build() const {
    // Need to sync the header before returning it so that changes will be reflected in the final product
    bcf_hdr_sync(m_header.get());
    return VariantHeader{move(m_header)};
  }

 private:
  std::shared_ptr<bcf_hdr_t> m_header;

};

}

#endif // gamgee__variant_header_builder__guard