- general_assert(n_targets == M, "Number of transcripts does not match! Please check if the reads are aligned to a transcript set (instead of a genome)!");
+ general_assert(n_targets == M, "Number of reference sequences does not match! Please check if the reads are aligned to a transcript set (instead of a genome)!");
dict.clear();
for (int i = 1; i <= M; i++) {
dict.clear();
for (int i = 1; i <= M; i++) {
- const std::string& tid = transcripts[i].getTranscriptID();
+ const std::string& tid = isAlleleSpecific() ? transcripts[i].getSeqName() : transcripts[i].getTranscriptID();
iter = dict.find(tid);
iter = dict.find(tid);
- assert(iter == dict.end());
+ general_assert(iter == dict.end(), tid + " appears more than once!");