#!/usr/bin/env Rscript
# =============================================================================
# run_virfinder.R
# Score contigs for "virusness" with VirFinder and write a sorted TSV.
#
# Usage:  Rscript run_virfinder.R <contigs.fa> <output.tsv>
#
# VirFinder returns a score (0-1) and a p-value per contig. Treat it as ONE
# line of evidence: confirm candidates with VirSorter2/geNomad + CheckV.
# =============================================================================

args <- commandArgs(trailingOnly = TRUE)
if (length(args) != 2) {
  stop("Usage: Rscript run_virfinder.R <contigs.fa> <output.tsv>")
}
contigs <- args[1]
out_tsv <- args[2]

suppressMessages(library(VirFinder))

pred <- VF.pred(contigs)
# Lower p-value = stronger viral signal; sort so best candidates are on top.
pred <- pred[order(pred$pvalue), ]

dir.create(dirname(out_tsv), showWarnings = FALSE, recursive = TRUE)
write.table(pred, file = out_tsv, sep = "\t", quote = FALSE, row.names = FALSE)
cat("Wrote", nrow(pred), "scored contigs to", out_tsv, "\n")