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#include "GBase.h"
#include "GArgs.h"
#include "GStr.h"
#define USAGE "Usage:\n\
mdtest '<MD-string>' \n\
Shows an example of basic parsing of a MD string.\n\
"
int main(int argc, char* argv[]) {
GArgs args(argc, argv, "h");
int numargs=args.startNonOpt();
if (args.getOpt('h') || numargs!=1) {
GMessage("%s\n",USAGE);
exit(0);
}
char* mdstr=args.nextNonOpt();
//--make a copy of the string, in case the original is a const string
// (because the parseUInt() function modifies the string temporarily
char* mdstring=Gstrdup(mdstr);
char *p=mdstring;
while (*p!='\0') {
int num_matches=0;
if (parseInt(p,num_matches)) {
if (num_matches!=0)
GMessage("%d matching bases\n", num_matches);
continue;
}
if (*p=='^') { //deletion
GDynArray<char> deletion; //deletion string accumulates here (if needed)
int del_length=0;//tracking deletion length
char delbase=*(++p);
while (delbase>='A' && delbase<='Z') {
deletion.Add(delbase);
del_length++;
delbase=*(++p);
}
GMessage("%d base(s) deletion [", del_length);
for (uint i=0;i<deletion.Count();++i) GMessage("%c",deletion[i]);
GMessage("]\n");
continue;
}
if (*p>='A' && *p<='Z') {
GMessage("base mismatch [%c]\n",*p);
p++;
continue;
}
GMessage("Warning: skipping unrecognized char [%c]\n", *p);
p++;
}
GFREE(mdstring);
return 0;
}
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