Change order of if statements for running genoprob command

Now it checks for pairscan first, just in case interval ends up being
passed (which is an irrelevant parameter for pairscan)

Also added a couple more verbose prints

1 files changed, 6 insertions, 4 deletions

diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index fb12012..5ecd774 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -172,12 +172,12 @@ verbose_print('Generating cross object\n')
 cross_object = geno_to_csvr(geno_file, trait_names, trait_vals, cross_file, type)
 
 # Calculate genotype probabilities
-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)) {
+if (!is.null(opt$pairscan)) {
   verbose_print('Calculating genotype probabilities for pair-scan\n')
   cross_object <- calc.genoprob(cross_object, step=10)
+} else if (!is.null(opt$interval)) {
+  verbose_print('Calculating genotype probabilities with interval mapping\n')
+  cross_object <- calc.genoprob(cross_object, step=5, stepwidth="max")
 } else {
   verbose_print('Calculating genotype probabilities\n')
   cross_object <- calc.genoprob(cross_object)
@@ -241,10 +241,12 @@ if (!is.null(opt$control)) {
 }
 
 if (!is.null(opt$pairscan)) {
+  verbose_print("Running scantwo")
   scan_func <- function(...){
     scantwo(...)
   }
 } else {
+  verbose_print("Running scanone")
   scan_func <- function(...){
     scanone(...)
   }