From 2cb18bb7916e029d3aa7779df710c1d0cbc910f8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 2 Aug 2021 21:07:52 +0000
Subject: Updated rqtl_wrapper to also return a map file when doing a pair-scan
 (since we need the list of markers/pseudomarkers and their positions)

---
 scripts/rqtl_wrapper.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'scripts/rqtl_wrapper.R')

diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index ebd5a91..ffff5b9 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -157,7 +157,7 @@ if (!is.null(opt$interval)) {
   verbose_print('Calculating genotype probabilities with interval mapping\n')
   cross_object <- calc.genoprob(cross_object, step=5, stepwidth="max")
 } else if (!is.null(opt$pairscan)) {
-  verbose_print('Calculating genotype probabilities with interval mapping\n')
+  verbose_print('Calculating genotype probabilities for pair-scan\n')
   cross_object <- calc.genoprob(cross_object, step=10)
 } else {
   verbose_print('Calculating genotype probabilities\n')
@@ -246,7 +246,9 @@ if (!is.null(opt$addcovar) || !is.null(opt$control)){
 
 verbose_print('Writing results to CSV file\n')
 if (!is.null(opt$pairscan)) {
+  map_out_file = file.path(opt$outdir, paste("MAP_", opt$filename, sep = "" ))
   write.csv(qtl_results[1], out_file)
+  write.csv(qtl_results[2], map_out_file)
 } else {
   write.csv(qtl_results, out_file)
 }
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