BamHeader.h

#ifndef theplu_yat_omic_bam_header
#define theplu_yat_omic_bam_header

// $Id: BamHeader.h 3550 2017-01-03 05:41:02Z peter $

/*
  Copyright (C) 2012, 2013, 2014, 2015, 2016 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  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 this program. If not, see <http://www.gnu.org/licenses/>.
*/

#include "config_bam.h"

#include "yat/utility/config_public.h"

#include "yat/utility/stl_utility.h"

#include YAT_SAM_HEADER

#include <boost/iterator/transform_iterator.hpp>

#include <map>
#include <string>

namespace theplu {
namespace yat {
namespace omic {

#ifndef YAT_HAVE_HTSLIB
  namespace detail {
    bam_header_t * bam_hdr_dup(const bam_header_t* other);
  }
#endif

  class BamHeader
  {
    typedef std::map<std::string, std::string> strMap;
    typedef std::map<std::string, strMap> strMap2;
  public:
    BamHeader(void);

    ~BamHeader(void);

    BamHeader(const BamHeader&);

    void parse_region(const std::string& reg, int& tid, int& begin,
                      int& end) const;

    const std::string& program_group(const std::string& id,
                                     const std::string& key) const;

    const std::string& read_group(const std::string& id,
                                  const std::string& key) const;

    const std::map<std::string, std::string>&
    read_group(const std::string& id) const;

    typedef boost::transform_iterator<
      utility::PairFirst<const strMap2::value_type>,
      strMap2::const_iterator>
    read_group_iterator;

    read_group_iterator read_group_begin(void) const;

    read_group_iterator read_group_end(void) const;

    void swap(BamHeader& other);

    const char* target_name(size_t tid) const;

    uint32_t target_length(size_t tid) const;

    std::string text(void) const;

    void text(const std::string& txt);

    int32_t tid(const std::string& name) const;

    int32_t n_targets(void) const;

    BamHeader& operator=(const BamHeader& rhs);

  private:
#ifndef YAT_HAVE_HTSLIB
    typedef bam_header_t bam_hdr_t;
#endif
    bam_hdr_t* header_;
    mutable strMap2 read_group_;
    mutable strMap2 program_group_;

    friend class InBamFile;
    friend class OutBamFile;

    const std::string& group(strMap2& map, const std::string& type,
                             const std::string& id,
                             const std::string& key) const;

    void update_group(strMap2& map, const std::string& type) const;

    // using compiler generated copy and assignment
  };

  void swap(BamHeader& lhs, BamHeader& rhs);

}}}
#endif