X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=preRef.cpp;h=e2f03269ba44d2ff9e0cb5601c3b4c6d1a3d9435;hp=7518ec41d184be27a637af8f756e7c6d46f6e32f;hb=refs%2Fheads%2Fdebian;hpb=a1dc3c6c442d288c7f4218cbb8b7a54f08e9d980

diff --git a/preRef.cpp b/preRef.cpp
index 7518ec4..e2f0326 100644
--- 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");
@@ -42,23 +41,19 @@ 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);
 	}
 
 	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; }
 	}
 
@@ -73,21 +68,21 @@ 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(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;
 }