Porkchop library-preparation QC evidence

These functions call the curated ../porkchop Rust library in-process and return R-native evidence tables for nanopore library-preparation QC, review, reporting, and synoptikon handoff. They do not call the Porkchop CLI, trim reads, demultiplex reads, or write preprocessing outputs. Public default builds keep Porkchop unlinked until that dependency is publicly available; in that mode these wrappers raise typed R conditions.

Usage

library_kit_candidates(reads, read_ids = NULL)

library_adapter_primer_evidence(reads, kit_id, read_ids = NULL)

library_barcode_evidence(reads, kit_id, read_ids = NULL)

library_cdna_primer_evidence(reads, kit_id, read_ids = NULL)

Arguments

reads

Character vector of read sequences, or a data frame with read_id and sequence columns.

read_ids

Optional character vector of read identifiers. Ignored when reads is a data frame with a read_id column.

kit_id

Character scalar. Porkchop kit identifier, such as LSK114, NBD114.24, or PCS114.

Value

library_kit_candidates() returns a data frame with kit metadata, provenance, support-level, validation-status, score, normalized_score, and score_kind columns.

library_adapter_primer_evidence() and library_barcode_evidence() return one row per motif hit.

library_cdna_primer_evidence() returns one row per read with cDNA class and primer-pair evidence columns.

Details

Porkchop scores are heuristic evidence scores, not calibrated probabilities. The score_kind column is therefore always "heuristic_evidence_score". Kit registry support, lifecycle status, support level, provenance, validation status, and known limitations are carried into the returned tables where applicable.

Examples

if (flounder_rust_capabilities(required = FALSE)$porkchop == "linked") {
  library_kit_candidates(c("TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT"))
}

if (flounder_rust_capabilities(required = FALSE)$porkchop == "linked") {
  library_adapter_primer_evidence(
    reads = c("TTTTTTTTCCTGTACTTCGTTCAGTTACGTATTGCT"),
    kit_id = "LSK114"
  )
}

if (flounder_rust_capabilities(required = FALSE)$porkchop == "linked") {
  library_barcode_evidence(
    reads = c("AAGGTTAACACAAAGACACCGACAACTTTCTTCAGCACCT"),
    kit_id = "NBD114.24"
  )
}

if (flounder_rust_capabilities(required = FALSE)$porkchop == "linked") {
  library_cdna_primer_evidence(
    reads = c(paste0(
      "TTTCTGTTGGTGCTGATATTGCTTTAAAATTAAAATTAAAATTAAAATTTGGG",
      "AAAA",
      "CTTGCCTGTCGCTCTATCTTCAGAGGAG"
    )),
    kit_id = "PCS114"
  )
}