saminfra.hh

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#pragma once
#include <string>
#include "antonie.hh"
#include <stdio.h>
#include "fastq.hh"


class SAMWriter
{
public:
  SAMWriter(const std::string& fname, const std::string& genome, dnapos_t len);
  ~SAMWriter();
  void write(dnapos_t pos, const FastQRead& fqfrag, int indel=0, int flags=0, const std::string& rnext="*", dnapos_t pnext=0, int32_t tlen=0 );
private:
  FILE* d_fp;
  std::string d_fname;
  std::string d_genomeName;
};