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#ifndef _BLASR_AMOS_AFG_BAS_WRITER_HPP_
#define _BLASR_AMOS_AFG_BAS_WRITER_HPP_
#include <cmath>
#include <fstream>
#include <sstream>
#include <pbdata/SMRTSequence.hpp>
class AfgBasWriter
{
// TODO correct file type? outFile
// TODO change SMRTSequence to FASTQ sequence? then maybe fasta2afg would be
// easier to write
std::string afgFileName;
std::ofstream afgOut;
bool firstRecord;
int recordCount;
int defaultQuality;
// Use 122 = '{' - 1 because '{' and '}' are the message delimiters in AMOS.
static const unsigned char maxAfgQuality = 122;
static const unsigned char charToQuality = 48;
static const unsigned char minAfgQuality = charToQuality + 1;
static const int lineLength = 80;
private:
unsigned char pacbioQVtoPhredQV(unsigned char pacbio);
public:
// Assume that closing the afg file must be done
// manually and not in a destructor.
~AfgBasWriter();
AfgBasWriter();
void Initialize(std::string _afgFileName);
void Close();
int Write(SMRTSequence &seq);
void SetDefaultQuality(int _defaultQuality);
private:
void WriteHeader();
void WriteOpen(void);
void WriteIdentifier(SMRTSequence &seq);
void WriteClose();
void WriteBases(SMRTSequence &seq);
void WriteQualities(SMRTSequence &seq);
};
#endif
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