source: trunk/yat/omic/BamHeader.h @ 2999

#ifndef theplu_yat_omic_bam_header
#define theplu_yat_omic_bam_header

// $Id: BamHeader.h 2999 2013-03-14 13:30:14Z peter $

/*
  Copyright (C) 2012, 2013 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 {

  /**
     Wrapper around bam_header_t struct.

     Class is typically created within InBamFile

     \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 = 99000 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 unexpected.

       \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