PhredPhd.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_IO_PHREDPHD_H
#define BPP_SEQ_IO_PHREDPHD_H
 
 
#include "../Sequence.h"
#include "../SequenceWithQuality.h"
#include "ISequenceStream.h"
 
namespace bpp
{
class PhredPhd : public ISequenceStream
{
public:
  PhredPhd() {}
 
  virtual ~PhredPhd() {}
 
public:
  bool nextSequence(
      std::istream& input,
      Sequence& seq
      ) const;
  bool nextSequence(
      std::istream& input,
      Sequence& seq,
      std::vector<size_t>& pos
      ) const;
 
  const std::string getDataType() const { return "SequenceWithQuality"; }
  const std::string getFormatName() const { return "phd file"; }
  const std::string getFormatDescription() const
  {
    return "Sequences following the phd format as describe in the phred documentation.";
  }
private:
  bool parseFile_(std::istream& input, std::string& name, std::string& sequence, std::vector<int>& qual, std::vector<size_t>& pos) const;
 
  bool parseDNA_(std::istream& input, std::string& sequence, std::vector<int>& qual, std::vector<size_t>& pos) const;
};
} // end of namespace bpp
#endif // BPP_SEQ_IO_PHREDPHD_H