released/pIRS.old/stat_illumina_reads/gcvgstater/stat_soap_coverage.h

   1 #ifndef _STAT_SOAP_COVERAGE_H
   2 #define _STAT_SOAP_COVERAGE_H
   3 #include <string>
   4 //#include <pair>
   5 #include <map>
   6 #include <vector>
   7 #include <stdint.h>
   8 using namespace std;
   9
  10 class stat_soap_coverage
  11 {
  12     private:
  13         string str_ref_file_name;
  14         string str_output_prefix;
  15         vector<string> vec_soap_file_name;
  16         vector<string> vec_width;
  17         bool b_gcdump;
  18         bool b_depwindump;
  19         map<string, string> map_reference_base;
  20         map<string, vector<unsigned int> > map_soap_coverage;
  21         map<int, map<double, vector<double> > > map_width_soap_gc_depth;
  22         map<int, vector<double> > map_gc_keyname;
  23         map<string, vector<double> > map_stat_coverage;
  24         map<int, uint64_t> map_sumwincount;
  25         map<int, uint64_t> map_sumdepthcount;
  26         map<int, map<double, uint64_t> >map_wincount;
  27         map<double, map<string, uint64_t> > map_stat_depth;
  28         vector<string> vec_chr_keyname;
  29         map<int, uint64_t> winCountN;
  30
  31     public:
  32         stat_soap_coverage(string str_ref_file_name, string str_output_prefix,
  33                 vector<string> vec_soap_file_name, vector<string> vec_width,
  34                 bool b_gcdump = false, bool b_depwindump = false);
  35         void DealReference();
  36         void DealSoapCoverage();
  37         void DealStat();
  38         void StatGC();
  39         void statDepth();
  40         void StatCoverage();
  41         void Run();
  42         ~stat_soap_coverage();
  43 };
  44 #endif