 
         if (data_mask & AlignmentDataMask::MATE_CHROMOSOME)
         {
+            // note: for the mate chromosome we don't bail out if the sequence doesn't exist
             std::string sequence_name = get_sequence_name(data->core.mtid);
             const bool seq_valid = reference->make_sequence_available(sequence_name);
 

                batch->chromosome.push_back(seq_id);
                batch->chromosome_map.mark_resident(seq_id);
            } else {
                fprintf(stderr, "ERROR: sequence %s not found in reference file\n", sequence_name.c_str());
                exit(1);
            }
        }



        if (data_mask & AlignmentDataMask::CHROMOSOME)
        {
            uint32 tid = data->core.tid;
            std::string sequence_name = get_sequence_name(tid);
            const bool seq_valid = reference->make_sequence_available(sequence_name);

            if (seq_valid)
