released/pIRS.old/pIRS_simulator/simulate.h

   1 #ifndef __SIMULATE_H_
   2 #define __SIMULATE_H_
   3
   4 using namespace std;
   5
   6 extern char alphabet[128];
   7 extern char alphabet2[128];
   8 extern char Bases[5];
   9 extern char c_bases[5];
  10
  11 //check whether a sequence contain non base characters, such as "N"
  12 int check_seq (string &seq);
  13
  14 //find random number location
  15 int search_location(double *Arr, uint64_t ArrNum, double random_num);
  16
  17 //simulate normal distribution insertsize by Box-muller method
  18 int simulate_insertsize(int mean, int sd);
  19
  20 //simulate GC bias
  21 int simulate_GC_bias(string insert_str, double *GC_bias_abundance);
  22
  23 //Realization of snp
  24 char get_snp_match(char base, double snp_bias[]);
  25
  26 //Getting insert sequence when heterozygous indel rate is bigger than 0
  27 string get_insertion(int num);
  28
  29 //get the reverse and complement sequence
  30 string reversecomplementary (string read);
  31
  32 //Produce heterozygous SNPs
  33 string Get_snp(string &seq,ofstream &snp,string id, double hetersnp_rate, double snp_bias[]);
  34
  35 //Getting invert sequence
  36 string Get_invertion(string &seq, ofstream &invertion_file, string id, double SV_rate);
  37
  38 //Getting indel sequence
  39 string Get_indel(string &seq,ofstream &indel,string id1,double heterindel_rate,double SV_rate);
  40
  41 #endif