source: trunk/yat/omic/BamHeader.h @ 2883

#ifndef theplu_yat_omic_bam_header
#define theplu_yat_omic_bam_header

// $Id: BamHeader.h 2883 2012-12-03 12:48:51Z peter $
//
// Copyright (C) 2012 Peter Johansson
//
// This program 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.
//
// This program 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 <bam.h>

namespace theplu {
namespace yat {
namespace omic {

  /**
     Wrapper around bam_header_t struct.

     Class is typically created within InBamFile
   */
  class BamHeader
  {
  public:
    /**
       \brief Default constructor
     */
    BamHeader(void);

    /**
       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;

    /**
       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