The current naming strategy has two problems:

1. The usage of the CIGAR and MD strings does not provide a name for isomiRs with a 1-to-1 relation between the name the sequence it represents. Therefore, the results can contain 1-to-many relations.
2. The start and end position shifts are not computed correctly creating incorrect names and possibly swapping canonical miRNA and isomiRs.

In order to solve this issue, the script iso_name_tagging.py needs to be refactor knowing exactly the values (if 0-based or 1-based) of the start and end positions in both the input files and the tools used.
In addition, find a new naming convention that ensure 1-to-1 relationships between the isomiR and the sequence it represents and apply it in that same script.