Pre-compute a whole-genome pairwise alignment of a sample against its BLAST reference and write the result for ingestion into the blast_ref_alignment SQLite table.

Called from the blast_ref_align Nextflow process after annotation is complete. Both sequences are passed as plain nucleotide strings (no headers, no line-breaks) so that this function can run entirely from file-based inputs without a database connection.

Usage

compute_blast_ref_alignment(assembly_seq, ref_seq, rotation = 0L, output_file)

Arguments

assembly_seq

nucleotide sequence string for the sample assembly

ref_seq

nucleotide sequence string for the BLAST reference genome

rotation

integer offset (0-based) used to rotate the reference so that it starts at the same anchor gene as the sample assembly. Equals pos1 - 1 of the anchor gene in the reference's blast_ref_annotations record.

output_file

path to write a one-row CSV with columns aligned_sample, aligned_ref, rotation, ref_length