Generated two index multi-Fasta files instead, one without 'N' converted to 'G' and...

[rsem.git] / preRef.cpp

diff --git a/preRef.cpp b/preRef.cpp
index 7518ec41d184be27a637af8f756e7c6d46f6e32f..da6c84e3122730e2f72e1c699e5629d8ed27aed2 100644 (file)
--- a/preRef.cpp
+++ b/preRef.cpp
@@ -23,18 +23,17 @@ PolyARules rules;
 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");
@@ -42,9 +41,7 @@ int main(int argc, char* argv[]) {
                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);
        }
 
@@ -58,7 +55,6 @@ int main(int argc, char* argv[]) {
        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; }
        }
 
@@ -73,21 +69,21 @@ int main(int argc, char* argv[]) {
        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(ng2_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;
 }