fastq.hh

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#pragma once
#include <string>
#include <stdio.h>
#include <stdint.h>
#include <stdexcept>

struct FastQRead
{
  FastQRead() : reversed(false), position(0) {}
  std::string d_nucleotides;
  std::string d_quality;
  std::string d_header;
  bool exceedsQuality(unsigned int);
  std::string getSangerQualityString() const;
  void reverse();
  bool reversed;
  uint64_t position; 
};

class FASTQReader
{
public:
  FASTQReader(const std::string& str, unsigned int qoffset, unsigned int snipLeft=0, unsigned int snipRight=0);

  void seek(uint64_t pos) 
  {
    fseek(d_fp, pos, SEEK_SET);
  }

  unsigned int getRead(FastQRead* fq); 
private:
  FILE *d_fp;
  unsigned int d_qoffset;
  unsigned int d_snipLeft, d_snipRight;
};

class StereoFASTQReader
{
public:
  StereoFASTQReader(const std::string& name1, const std::string& name2, 
                    unsigned int qoffset, unsigned int snipLeft=0, unsigned int snipRight=0) : d_fq1(name1, qoffset, snipLeft, snipRight), d_fq2(name2, qoffset, snipLeft, snipRight) 
  {}

  void seek(uint64_t pos);

  unsigned int getRead(uint64_t pos, FastQRead* fq2);
  unsigned int getReadPair(FastQRead* fq1, FastQRead* fq2);
private:
  FASTQReader d_fq1, d_fq2;
  constexpr static uint64_t s_mask = ~(1ULL<<63);
};