Changes v0.9.0 - 2026-03-13 New commands: lexicmap utils 2sam: Convert the default search output to SAM format (#26). Attention: This command requires search results generated by the current LexicMap version. lexicmap index: Added a new flag --soft-masking to support soft-masked genomes (usually eukaryotic genomes). Lowercase bases in soft-masked low-complexity regions will be treated as A's and won't be seeded, while they will be saved for base-level alignment. The value of this flag is appended to the index information file info.toml. Added a new option --max-kmer-freq. If a mask captures the same k-mer at more than N positions in a genome, only the first N positions will be retained. This option may reduce search sensitivity, but it can be useful when simply checking whether a query matches any position in a genome that contains many tandem repeat sequences. The value of this flag is appended to the index information file info.toml. Added sequence validity checking. #30 lexicmap search: Fixed the computation of bitscore and evalue. Previous values were slightly overestimated. Fixed CIGAR to follow the SAM spec. Previously, 'D' and 'I' were inverted. Fixed merging search results from genome chunks. Some were not merged. New flag -N/--top-n-chains for keeping the top N chains in a genome for the query (0 for all) in the chaining phase. It reduces search time when one needs only the most similar matches in a genome. Improved seed chaining speed and reduced the memory usage, especially for genomes with lots of repeat sequences. lexicmap utils subseq: Fixed a concurrency bug when using search result as the input. lexicmap utils genomes: Added a new flag -e/--extra to show more information. lexicmap utils masks: Changed the default values of -m/--masks and -p/--prefix to match those in lexicmap index.