Antonie
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00001 #pragma once 00002 #include <string> 00003 #include "antonie.hh" 00004 #include <stdio.h> 00005 #include "fastq.hh" 00006 00007 00009 class SAMWriter 00010 { 00011 public: 00012 SAMWriter(const std::string& fname, const std::string& genome, dnapos_t len); 00013 ~SAMWriter(); 00014 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 ); 00015 private: 00016 FILE* d_fp; 00017 std::string d_fname; 00018 std::string d_genomeName; 00019 };