Refs refs;
ofstream fout;
-char refF[STRLEN], alignerFastaF[STRLEN], transF[STRLEN];
+char refF[STRLEN], idxF[STRLEN], n2g_idxF[STRLEN];
int polyAChoice, polyALen;
char exceptionF[STRLEN];
-bool ntog; // true , change N into G; false do not change. Default is true.
bool quiet; // verbose = !quiet;
// always generate references for aligners, default convert all N into G
int main(int argc, char* argv[]) {
if (argc < 4) {
- printf("USAGE : rsem-preref refFastaF polyAChoice refName [-l polyALen] [-f exceptionF] [--no-ntog] [-q]\n\n");
+ printf("USAGE : rsem-preref refFastaF polyAChoice refName [-l polyALen] [-f exceptionF] [-q]\n\n");
printf(" refFastaF: a FASTA format file contains all reference transcripts\n");
printf(" polyAChoice: choice for polyA tail padding.It is a number from {0,1,2}\n");
printf(" 0: pad polyA tail\n");
printf(" 2: pad polyA tail for all references but those in exceptionF\n");
printf(" -l: polyALen: specify the length of polyA tail you want to pad. Default is 100\n");
printf(" -f: exceptionF: file contains a list of exception reference ids. IDs starts from 1. Must set if polyAChoice = 2\n");
- printf(" --no-ntog: do not convert N in references into G\n");
printf(" -q: quiet\n");
- printf(" This program will generate a file named \"refName.transcripts.fa\", which may rewrite an existing file (e.g. refFastaF).\n");
exit(-1);
}
polyAChoice = atoi(argv[2]);
polyALen = 125;
- ntog = true;
quiet = false;
memset(exceptionF, 0, sizeof(exceptionF));
for (int i = 4; i < argc; i++) {
if (!strcmp(argv[i], "-l")) { polyALen = atoi(argv[i + 1]); }
if (!strcmp(argv[i], "-f")) { strcpy(exceptionF, argv[i + 1]); }
- if (!strcmp(argv[i], "--no-ntog")) { ntog = false; }
if (!strcmp(argv[i], "-q")) { quiet = true; }
}
sprintf(refF, "%s.seq", argv[3]);
refs.saveRefs(refF);
- sprintf(transF, "%s.transcripts.fa", argv[3]);
- fout.open(transF);
+ sprintf(idxF, "%s.idx.fa", argv[3]);
+ fout.open(idxF);
for (int i = 1; i <= M; i++) {
fout<< ">"<< refs.getRef(i).getName()<< endl<< refs.getRef(i).getSeq()<< endl;
}
fout.close();
- if (verbose) printf("%s is generated!\n", transF);
+ if (verbose) printf("%s is generated!\n", idxF);
- sprintf(alignerFastaF, "%s.idx.fa", argv[3]);
- fout.open(alignerFastaF);
+ sprintf(n2g_idxF, "%s.n2g.idx.fa", argv[3]);
+ fout.open(n2g_idxF);
for (int i = 1; i <= M; i++) {
- fout<<">"<<refs.getRef(i).getName()<<endl<<(ntog ? aligner_refp.convert(refs.getRef(i).getSeq()) : refs.getRef(i).getSeq())<<endl;
+ fout<< ">"<< refs.getRef(i).getName()<< endl<< aligner_refp.convert(refs.getRef(i).getSeq())<< endl;
}
fout.close();
- if (verbose) printf("%s is generated!\n", alignerFastaF);
+ if (verbose) printf("%s is generated!\n", n2g_idxF);
return 0;
}