Find the Transcripts Whose Coding Sequence Events Overlap — rduckvep_coding

The fast discovery route into [rduckvep_haplotypes()]: one native lookup in the resident transcript interval index and exon layout instead of annotating every record. Each row of `events_query` is one VCF record and one ALT allele with its shared anchor base (`reference`, `alternate`, one-based `position`); the event is normalized exactly as the annotation builder normalizes it, so the pairs returned are exactly those to which [rduckvep_annotate()] assigns the CDS region bit: an indel's anchor base alone never creates an overlap, an insertion is placed on the base the annotation builder places it on (and is not a CDS event at the outer CDS edges), and an intron of at most 13 bases inside the CDS counts as coding. Symbolic and breakend ALTs, missing ALTs and alleles identical to REF are not events. Records with no coding overlap, the large majority of a genome, produce no rows, so a VCF reduces to its coding records before any per-record work. The result is the `transcript_index` column of a calls relation for [rduckvep_haplotypes()]: join it with the records' genotypes.

Usage

rduckvep_coding_transcripts(
  con,
  events_query,
  model_name,
  table_name = NULL,
  overwrite = FALSE
)

Arguments

con: An open DuckDB connection with DuckVEP loaded.
events_query: One nonempty SELECT query supplying `event_index`, `seq_region`, `position`, `reference` and `alternate` (any integer types for the first three).
model_name: Name of an already loaded DuckVEP model without wrapped circular objects.
table_name: Optional output table name.
overwrite: Whether to replace an existing output table.

Value

A data frame of `event_index` and `transcript_index` (one row per pair, ascending by transcript within an event), or invisible `TRUE` when creating `table_name`.