int main(int argc, char **argv){
FILE *in;
char fname[100];
char *kmer;
int i,j;
char seqname[50];
char ch;
char dummy[100];
int seqlen;
int klen;
fname[0] = 0;
for (i=0;i<argc;i++){
if (!strcmp(argv[i], "-i"))
strcpy(fname, argv[i+1]);
else if (!strcmp(argv[i], "-s")){
kmer = (char *) malloc(sizeof(char) * strlen(argv[i+1]));
strcpy(kmer, argv[i+1]);
for (j=0;j<strlen(kmer);j++)
kmer[j] = toupper(kmer[j]);
}
}
if (fname[0] == 0 || kmer[0] ==0)
return 0;
in = fopen(fname, "r");
fscanf(in, "%c", &ch);
fscanf(in, "%s", seqname);
fgets(dummy, 100, in);
i=0;
while(fscanf(in, "%c", &ch) > 0){
if (!isspace(ch))
seq[i++]=toupper(ch);
}
seq[i]=0;
seqlen=i;
klen = strlen(kmer);
for(i=0;i<seqlen-klen+1;i++){
if (match(i, seq, kmer))
printf("%s\t%d\t%d\tF\n", seqname, (i+1), (i+1+klen));
else if (match_r(i, seq, kmer))
printf("%s\t%d\t%d\tR\n",seqname, (i+1), (i+1+klen));
}
return 1;
}
/*
* The run_benchmarks function will run the registered benchmarks.
*/
void run_benchmarks(const options& opts) {
std::regex match_r(opts.get_bench());
auto benchmarks = registration::get_ptr()->get_benchmarks();
for (auto& info : benchmarks) {
if (std::regex_match(info.get_name(), match_r)) {
context c(info, opts);
auto r = c.run();
std::cout << std::setw(35) << std::left << info.get_name() << r.to_string() << std::endl;
}
}
}
