454ITS数据按barcode和primer分类程序v1.0

不知道有什么好办法可以让primer允许漏配，现在仅仅是允许错配，还是有一些没有配上，454数据有些primer漏配了一些，下一步解决这个问题

 #include <cstdio>
 #include <cstdlib>
 #include <string>
 #include <iostream>
 #include <fstream>
 #include <iomanip>
 #include <getopt.h>
 using namespace std;

 int max_mis = ;
 int N = ;
 string primer = "";
 string* barcode = NULL;
 string* barcodeName = NULL;
 void usage ()
 {
         cout << "\nUsage: splitByBarcode [options] <read.fasta> <barcode.txt> <output prefix>\n"
         << "  -m <int>  allow the max mis num, default " << max_mis << "\n"
     << "  -p <string> primer, required    "<<endl
     << "  -n <int>  barcode num, required"<<endl;
         exit();
 }
 struct COMPARE{
     int ifCompared;
     int posStart;
     int posEnd;
 };
 COMPARE compare(string reads, string barcode, int maxmis,int b,int e);
 int main(int argc, char *argv[])
 {
     if (argc < )
     {
         usage();
     }
     int c;
     while ((c=getopt(argc,argv,"m:n:p:")) != -)
     {
         switch (c)
         {
             case 'm' : max_mis = atoi(optarg);break;
             case 'n' : N = atoi(optarg); break;
             case 'p' : primer = optarg;break;
             default  : cout<<"error:"<<(char)c<<endl;usage();
         }
     }
     if(N<=){
         cerr<<"please input the required barcode num\n";
         exit();
     }
     if(primer == ""){
         cerr<<"please input the required primer\n";
         exit();
     }
     string seq_file = argv[optind++];
     string barcode_file = argv[optind++];
     string outPrefix = argv[optind++];
     string out_file = outPrefix + ".list";
     barcode = new string[N];
     barcodeName = new string[N];

     for(int i=;i<N;i++){
         barcodeName[i] = "";
         barcode[i] = "";
     }

     ifstream reads;
     reads.open(seq_file.c_str());
     if(!reads){
         cerr<<"fail to open input file"<<seq_file<<endl;
     }
     ifstream barcode_in;
     barcode_in.open(barcode_file.c_str());
     if(!barcode_in){
         cerr<<"fail to open barcode file" <<barcode_file<<endl;
     }

     string text;
     int k=;
     while( getline( barcode_in, text, '\n') )
     {
         int startPos = , endPos;
         endPos = text.find("\t");
         barcodeName[k] = text.substr(startPos, endPos-startPos+);
         startPos = endPos + ;
         endPos = text.find("\t",startPos);
         barcode[k] = text.substr(startPos, endPos-startPos+);
         //cout << barcodeName[k] <<"\t"<< barcodeForward[k] <<"\t"<< barcodeReverse[k] << endl;
         k++;
     }

     ofstream splitlist;
     splitlist.open(out_file.c_str());
     if(!splitlist){
         cerr<<"fail to creat output file" << out_file <<endl;
     }
     int line_num = ;
     splitlist<<"barcodeName\tid\tid_line\n";
     while( getline( reads, text, '\n') )
     {
         string seq = "", id = "";
         id = text;
         getline( reads, text, '\n');
         seq = text;

         COMPARE p1 ,p2;
         p1.ifCompared = p2.ifCompared = ;
         for(int k=;k<N;k++){
             p1 = compare(seq,primer,max_mis,,seq.length()-primer.length()+);
             if( p1.ifCompared )
             {
                 p2 = compare(seq,barcode[k],,,p1.posStart);
                 if ( p2.ifCompared ){
                 //cout<<seq1<<"\t"<<barcodeForward[k]<<"\t"<<seq2<<"\t"<<barcodeReverse[k]<<endl;
                     splitlist<<barcodeName[k]<<"\t"<<id<<"\t"<<line_num<<endl;
                     break;
                 }
             }
         }
         line_num = line_num + ;
     }
     delete[] barcode;
     delete[] barcodeName;
     splitlist.close();
     barcode_in.close();
     reads.close();
 }
 COMPARE compare(string reads, string barcode, int maxmis, int b, int e)
 {
     COMPARE p;
     //cout<<b<<"\t"<<e<<endl;
 //    cout<<barcode<<"\t"<<barcode.length()<<endl;
     for(int i=b;i<e;i++)
     {
         int mismatch = ;
         int pos = ;
         while(mismatch <= maxmis ){
             if(reads[i+pos] != barcode[pos]) mismatch++;
             pos++;
             if(pos == barcode.length()){
                 p.posStart = i;
                 p.posEnd = i+pos;
             //    cout<<p.posStart<<"\t"<<p.posEnd<<endl;
                 p.ifCompared = ;
                 return p;
             }
         }
     }
     p.ifCompared = ;
     return p;
 }