From 680a7c005bd364b9052d5ec6def39cdc676d6066 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Thu, 3 Oct 2024 16:19:27 +1000
Subject: [PATCH] cherrypick: manta -> sv (#173)

---
 inst/rmd/rnasum.Rmd | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/inst/rmd/rnasum.Rmd b/inst/rmd/rnasum.Rmd
index 15eb3e8d..fc1ceff5 100755
--- a/inst/rmd/rnasum.Rmd
+++ b/inst/rmd/rnasum.Rmd
@@ -1418,18 +1418,18 @@ fusions_ann <- RNAsum::fusions_annot(
 )
 ```
 
-```{r fusions_and_manta_data_prep, comment = NA, message=FALSE, warning=FALSE, eval = runSVsChunk}
-manta_sv <- sample_data.list[["wgs"]][["manta_tsv"]] |>
-  RNAsum::manta_process()
-tmp_sv_genes <- manta_sv$genes_all$Genes
+```{r fusions_and_sv_data_prep, comment = NA, message=FALSE, warning=FALSE, eval = runSVsChunk}
+sv <- sample_data.list[["wgs"]][["sv_tsv"]] |>
+  RNAsum::sv_process()
+tmp_sv_genes <- sv$genes_all$Genes
 tmp_expressed_sv_genes <- tmp_sv_genes[tmp_sv_genes %in% ref_dataset.list[[dataset]][["gene_annot_all"]]$SYMBOL]
 if (length(tmp_expressed_sv_genes) == 0) {
   # from now on don't evaluate SV chunks
   runSVsChunk <- FALSE
 }
 rm(tmp_sv_genes, tmp_expressed_sv_genes)
-##### Compare fusion genes called by MANTA
-##### First limit MANTA output to fusions only
+##### Compare fusion genes called by SV caller
+##### First limit SV output to fusions only
 if (runFusionChunk) {
   sv_fusions <- sv[["melted_variants"]] |>
     dplyr::filter(.data$is_fusion) |>