- Fixes for circular reference genomes - Memory corruption fixed - Filter for random short alignments added - Dynamic programming approach for choosing best combination of mapped segments (thanks to @bqminh) - Alignment computation speedup with SSE instructions (thanks to @smolkmo) - Mapping quality computation updates - Several memory leaks fixed - Small duplication detection improved - `--min-residues/-R` changed set to 25% (default). All reads that have less than 25% mapped are reported as unmapped per default - `--max-segments` added. Max number of segments reported for a single read