From 8556e33166d968f6e3a07ec50f7af78865c6c80e Mon Sep 17 00:00:00 2001
From: Arielle R Munters <45485665+elleira@users.noreply.github.com>
Date: Mon, 21 Aug 2023 11:04:42 +0200
Subject: [PATCH] fix: remove exomdepth output =1

---
 workflow/scripts/exomedepth_export.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/workflow/scripts/exomedepth_export.R b/workflow/scripts/exomedepth_export.R
index be0112c..4ceb800 100644
--- a/workflow/scripts/exomedepth_export.R
+++ b/workflow/scripts/exomedepth_export.R
@@ -7,7 +7,10 @@ cnv_call_df <- data.frame(
   )
 
 if (length(all.exons@CNV.calls) > 0) {
-
+  
+  # for compatability with alissa remove rows where there is no-change (reads.ratio == 1)
+  cnv_call_df <- cnv_call_df[cnv_call_df$reads.ratio != 1, ] 
+  
   # Create Nexus SV format text file
   nexus <- c("id", "reads.ratio")
   nexus_df <- cnv_call_df[nexus]