source: trunk/yat/omic/BamHeader.h @ 3410

#ifndef theplu_yat_omic_bam_header
#define theplu_yat_omic_bam_header

// $Id: BamHeader.h 3410 2015-04-21 23:05:43Z 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/utility/config_public.h"

#include YAT_SAM_HEADER

#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

  /**
     \brief Wrapper around bam_hdr_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);

    /**
       \brief Destructor
     */
    ~BamHeader(void);

    /**
       \brief Copy constructor
     */
    BamHeader(const BamHeader&);

    /**
       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;

    /**
       \brief Access value in \c \@PG lines.

       A program group line in the header typically looks like

       \code @PG  ID:bwa  PN:bwa  VN:0.6.1-r104 \endcode

       and for this line \c program_group("bwa", "VN") returns
       \c "0.6.1-r104"

       \return value for \a key for line with ID \a id.

       \since New in yat 0.13
    */
    const std::string& program_group(const std::string& id,
                                     const std::string& key) const;

    /**
       \brief Access value in \c \@RG lines.

       A read group line in the header typically looks like

       \code @RG  ID:foo  PL:ILLUMINA SM:Tumour \endcode

       and for this line \c read_group("foo", "SM") returns \c "Tumour"

       \return value for \a key for line with ID \a id.

       \since New in yat 0.13
    */
    //
    const std::string& read_group(const std::string& id,
                                  const std::string& key) const;

    /**
       \brief Exchanges the content in \c *this and \a other

       \since New in yat 0.13
     */
    void swap(BamHeader& other);

    /**
       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;

    /**
       \return text in header

       \since New in yat 0.13
     */
    std::string text(void) const;

    /**
       \brief set text in header

       This function parses \a txt and updates fields.

       \since New in yat 0.13
     */
    void text(const std::string& txt);

    /**
       \brief inverse of target_name(size_t)

       If compiled against libbam and \a name does not exist,
       behavious is undefined. If compiled against htslib, a
       utility::runtime_error is thrown.

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

    /**
       \return Number of chromosomes
     */
    int32_t n_targets(void) const;

    /**
       \brief assignment operator
     */
    BamHeader& operator=(const BamHeader& rhs);

  private:
#ifndef YAT_HAVE_HTSLIB
    typedef bam_header_t bam_hdr_t;
#endif
    bam_hdr_t* header_;
    typedef std::map<std::string, std::string> strMap;
    typedef std::map<std::string, strMap> strMap2;
    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;

    // using compiler generated copy and assignment
  };

  /**
     Exchanges the content in the headers.

     \since New in yat 0.13

     \relates BamHeader
   */
  void swap(BamHeader& lhs, BamHeader& rhs);

}}}
#endif