source: trunk/yat/omic/BamHeader.h @ 3188

#ifndef theplu_yat_omic_bam_header
#define theplu_yat_omic_bam_header

// $Id: BamHeader.h 3188 2014-03-25 10:24:29Z peter $

/*
  Copyright (C) 2012, 2013, 2014 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_BAM_HEADER

#include <string>

namespace theplu {
namespace yat {
namespace omic {

  /**
     \brief Wrapper around bam_header_t struct.

     Class is typically created via InBamFile::header().

     It is possible to copy and assign a BamHeader, but note that a
     BamHeader does not own underlying data. The underlying data is
     owned by the InBamFile and the BamHeader is thus invalid after
     the corresponding InBamFile has been destroyed.

     \since New in yat 0.10
   */
  class BamHeader
  {
  public:
    /**
       \brief Default constructor
     */
    BamHeader(void);

    /**
       Parse a region in the format: 'chr2:100,000-200,000 and return
       values in variables \a tid, \a begin and \a end. \a reg is
       1-based and \a begin and \a end are 0-based, i.e.,
       "chr2:100,000-200,000" will set \a begin = 99999 and \a end =
       200000.

       \see bam_parse_region

       \throw utility::runtime_error on failure

       \since new in yat 0.11
     */
    void parse_region(const std::string& reg, int& tid, int& begin,
                      int& end) const;

    /**
       Name of chromosome with ID \a tid
     */
    const char* target_name(size_t tid) const;

    /**
       Length of chromosome with ID \a tid
     */
    uint32_t target_length(size_t tid) const;

    /**
       \brief inverse of target_name(size_t)

       \note If \a name does not exist, behaviour is undefined.

       \since new in yat 0.11
     */
    int32_t tid(const std::string& name) const;

    /**
       Number of chromosomes
     */
    int32_t n_targets(void) const;
  private:
    bam_header_t* header_;

    friend class InBamFile;
    friend class OutBamFile;
    BamHeader(bam_header_t* h);

    // using compiler generated copy and assignment
    //BamHeader(const BamHeader&);
    //BamHeader& operator=(const BamHeader& rhs);
  };

}}}
#endif