Fasta.h

#ifndef _theplu_yat_omic_fasta
#define _theplu_yat_omic_fasta

// $Id: Fasta.h 3475 2016-03-08 08:05:33Z peter $
//
// Copyright (C) 2016 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 "config_bam.h"

#include YAT_FAIDX_HEADER

#include <boost/shared_array.hpp>
#include <boost/shared_ptr.hpp>

#include <map>
#include <string>
#include <vector>

namespace theplu {
namespace yat {
namespace omic {

  class Fasta
  {
  public:
    Fasta(const std::string& fn);

    bool present(const std::string& name) const;

    std::string name(size_t i) const;

    int nseq(void) const;

    int sequence_length(const std::string& name) const;

    class Sequence
    {
    public:
      typedef const char* const_iterator;

      const_iterator begin(void) const;

      const_iterator end(void) const;

      int size(void) const;

      char operator[](size_t i) const;
    private:
      friend class Fasta;
      friend Sequence reverse_complement(const Fasta::Sequence&);
      boost::shared_array<const char> seq_;
      int size_;
    };

    Sequence sequence(const std::string& chr) const;

    Sequence sequence(const std::string& chr, int beg, int end) const;

  private:
    boost::shared_ptr<faidx_t> faidx_;
    // using compiler generated copy
    //FastaIndex(const FastaIndex& other);
    //FastaIndex& operator=(const FastaIndex& rhs);
    void fetch(Sequence& seq, const std::string& chr, int begin, int end) const;
    // throw exception; called when incorrect chr is passed
    void throw_unknown_chr(const std::string&) const;
#ifndef YAT_HAVE_HTSLIB
    std::vector<std::string> name_;
    std::map<std::string, int> size_;
#endif
  };


  Fasta::Sequence reverse_complement(const Fasta::Sequence& sequence);
}}}
#endif