v1.0.1

• Added support for IUPAC nucleotide codes.
• Added a command-line interface (CLI).
• Enabled user control over the Smith–Waterman DP window size, allowing trade-offs between runtime and memory usage.
• Optimized alignment reconstruction by eliminating repeated string copying during recursive backtracking. Replaced per-call StringBuilder cloning with in-place updates and backtracking, reducing memory allocations and improving runtime performance, particularly for large edit distances during post-processing. This optimization was adapted from AutoFFinder.