VcfHeader.h

#ifndef theplu_yat_omic_vcf_header
#define theplu_yat_omic_vcf_header

// $Id: VcfHeader.h 3760 2018-10-18 04:43:18Z peter $

/*
  Copyright (C) 2018 Peter Johansson

  The yat library is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License as
  published by the Free Software Foundation; either version 3 of the
  License, or (at your option) any later version.

  The yat library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include <iosfwd>
#include <string>
#include <vector>

namespace theplu {
namespace yat {
namespace omic {

  class VcfHeader
  {
  public:
    VcfHeader(const std::string& version);

    VcfHeader(std::istream& is);

    void add(const std::string& key, const std::string& value);

    void add(const std::string& key, const std::string& ID, int number,
             const std::string& type, const std::string& description);

    void add_info(const std::string& ID, const std::string& number,
                  const std::string& type, const std::string& description);

    void add_format(const std::string& ID, const std::string& number,
                    const std::string& type, const std::string& description);

    void add_program_command(int argc, char* argv[]);

    void add_program_version(const std::string& prog,
                             const std::string& version);

    const std::string& header(void) const;

    void header(const std::string& header);

    const std::string& line(size_t i) const;

    std::string key(size_t line) const;

    void nicify(void);

    std::string value(size_t line) const;

    std::string value(size_t line, const std::string& key) const;

    size_t size(void) const;

    const std::vector<std::string>& samples(void) const;

    void samples(const std::vector<std::string>& s);

  private:
    friend std::ostream& operator<<(std::ostream& os, const VcfHeader& b);
    std::vector<std::string> lines_;
    mutable std::vector<std::string> samples_;

    void add(const std::string& key,
             const std::string& ID, const std::string& number,
             const std::string& type, const std::string& description);
    void key_value(size_t line, std::string& key, std::string& value) const;
    // remove line with ##KEY=<ID=id*
    void remove(const std::string& key, const std::string& id);

    // functor used in nicify
    struct Compare
    {
      bool operator()(const std::string& lhs, const std::string& rhs) const;
    private:
      int index(const std::string& s) const;
      bool match(const std::string& s, const std::string& prefix) const;
    };
  };

  std::ostream& operator<<(std::ostream&, const VcfHeader& header);

}}}

#endif