Removed '--no-bowtie' and '--no-ntog' options in 'rsem-prepare-reference' and put...

[rsem.git] / preRef.cpp

diff --git a/preRef.cpp b/preRef.cpp
index da6c84e3122730e2f72e1c699e5629d8ed27aed2..e2f03269ba44d2ff9e0cb5601c3b4c6d1a3d9435 100644 (file)
--- a/preRef.cpp
+++ b/preRef.cpp
@@ -48,7 +48,6 @@ int main(int argc, char* argv[]) {
        polyAChoice = atoi(argv[2]);
 
        polyALen = 125;
-       ntog = true;
        quiet = false;
        memset(exceptionF, 0, sizeof(exceptionF));
 
@@ -78,7 +77,7 @@ int main(int argc, char* argv[]) {
        if (verbose) printf("%s is generated!\n", idxF);
 
        sprintf(n2g_idxF, "%s.n2g.idx.fa", argv[3]);
-       fout.open(ng2_idxF);
+       fout.open(n2g_idxF);
        for (int i = 1; i <= M; i++) {
          fout<< ">"<< refs.getRef(i).getName()<< endl<< aligner_refp.convert(refs.getRef(i).getSeq())<< endl;
        }