- Removed dependency on external tssv package (it is no longer compatible). - Greatly increased performance by deduplicating the input reads. - Removed the -q/--is-fastq option in favour of automatic detection. - Changed the default value for -m/--mismatches from 0.08 to 0.1. - Changed the default value for -n/--indel-score from 1 to 2. - Added the -X/--no-deduplicate option to disable deduplication. - Fixed potential crash that could occur under very specific circumstances.