Matching embedded kmer tables to data

To make the alignment process as simple as possible, the user needs to provide POD5 file(s) and corresponding basecalls in a BAM file. Initially, also a kmer table was required, but since these are static a selection is now embedded in the executables.

The following tables are embedded:

Fishnet uses the basecall model name that is stored in the header of a BAM file generated by Dorado, more specifically in the basecall_model value of the DS tag (for more information see the Dorado docs).

The matching is performed in alignment::core::refinement::load_kmer_table. If no embedded kmer table can be matched to given data, the user is required to provide one manually using the --kmer-table flag.