This commit introduces sparse index support for KDI files to enable fast random access during k-mer matching. It adds a new .kdx index file format and updates the KDI reader and writer to handle index creation and seeking. The changes include:
- New KdxIndex struct and related functions for loading, searching, and writing .kdx files
- Modified KdiReader to support seeking with the new index
- Updated KdiWriter to create .kdx index files during writing
- Enhanced KmerSetGroup.Contains to use the new index for faster lookups
- Added a new 'match' command to annotate sequences with k-mer match positions
The index is created automatically during KDI file creation and allows for O(log N / stride) binary search followed by at most stride linear scan steps, significantly improving performance for large datasets.
