+ // Check if the reference used for aligner is the transcript set RSEM generated
+ if (refs.getM() != header->n_targets) {
+ fprintf(stderr, "Number of transcripts does not match! Please align reads against the transcript set and use RSEM generated reference for your aligner!\n");
+ exit(-1);
+ }
+ for (int i = 0; i < header->n_targets; i++) {
+ const RefSeq& refseq = refs.getRef(i + 1);
+ // If update int to long, chance the (int) conversion
+ if (refseq.getName().compare(header->target_name[i]) != 0 || refseq.getTotLen() != (int)header->target_len[i]) {
+ fprintf(stderr, "Transcript information does not match! Please align reads against the transcript set and use RSEM generated reference for your aligner!\n");
+ exit(-1);
+ }
+ }
+