From 82e1c0441ce702ae8881a9a5c6f386cdeeae19c1 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Wed, 5 Feb 2025 12:13:52 +0300
Subject: feat: Add the physical map file path.

---
 scripts/rqtl2_wrapper.R | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'scripts')

diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R
index 69606b2..5ad812e 100644
--- a/scripts/rqtl2_wrapper.R
+++ b/scripts/rqtl2_wrapper.R
@@ -514,6 +514,7 @@ for (chr in chr_names(cross)){
 
 
 gmap_file <- file.path(opt$directory, json_data$geno_map_file)
+pmap_file <- file.path(opt$directory, json_data$physical_map_file)
 output = list(lod_peaks = lod_peaks,
              scan_results =scan_results,
 	     genetic_probabilities = Pr,
@@ -526,6 +527,7 @@ output = list(lod_peaks = lod_peaks,
 	     chromosomes  = chr_names(cross),
 	     error_lod = error_lod,
 	     gmap_file = gmap_file,
+	     pmap_file = pmap_file, 
 	     meffects_plots = meffects_plots,
 	     lod_plot_path =lod_plot_path,
 	     scan_method = SCAN_METHOD  
-- 
cgit 1.4.1