From 353b7564d40223cc2b73d235a9d0b7721920a72b Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Wed, 25 Sep 2024 18:14:54 +1000
Subject: [PATCH] handle VAF_TUMOR and ACTIONABILITY_TIER from PCGR v2

---
 R/pcgr.R | 30 +++++++++++++++++++++++-------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/R/pcgr.R b/R/pcgr.R
index d5a07a54..30e1db9a 100644
--- a/R/pcgr.R
+++ b/R/pcgr.R
@@ -1,7 +1,8 @@
-#' Read PCGR Tiers TSV File
+#' Read PCGR TSV File
 #'
-#' Reads the `snvs_indels.tiers.tsv` file output by PCGR.
-#' @param x Path to PCGR `snvs_indels.tiers.tsv` file.
+#' Reads the `snvs_indels.tiers.tsv` (or v2's `snv_indel_ann.tsv.gz`) file output
+#' by PCGR.
+#' @param x Path to PCGR `snvs_indels.tiers.tsv`/`snv_indel_ann.tsv.gz` file.
 #' @return A tibble with the contents of the input TSV file, or NULL if x is NULL.
 #'
 #' @examples
@@ -24,10 +25,25 @@ pcgr_tiers_tsv_read <- function(x = NULL) {
         .default = "c"
       )
     )
-
-  assertthat::assert_that(
-    all(c("CONSEQUENCE", "TIER", "AF_TUMOR") %in% colnames(d))
-  )
+  assertthat::assert_that("CONSEQUENCE" %in% colnames(d))
+  if (!"TIER" %in% colnames(d)) {
+    if ("ACTIONABILITY_TIER" %in% colnames(d)) {
+      # ACTIONABILITY_TIER does not have TIER prefix
+      d <- d |>
+        dplyr::rename(TIER = "ACTIONABILITY_TIER") |>
+        dplyr::mutate(TIER = paste0("TIER ", .data$TIER))
+    } else {
+      stop("PCGR output does not contain TIER or ACTIONABILITY_TIER column!")
+    }
+  }
+  if (!"AF_TUMOR" %in% colnames(d)) {
+    if ("VAF_TUMOR" %in% colnames(d)) {
+      d <- d |>
+        dplyr::rename(AF_TUMOR = "VAF_TUMOR")
+    } else {
+      stop("PCGR output does not contain AF_TUMOR or VAF_TUMOR column!")
+    }
+  }
 
   d |>
     dplyr::mutate(