mskcc/facets-suite

Bug in normDepth.R

soccin opened this issue · 1 comments

In normDepth.R You have an undefined variable "filename" here:

if(!interactive()){
  parser = ArgumentParser()
  parser$add_argument('-f', '--file', type='character', help='Filename of counts file to be normalized.')
  args=parser$parse_args()
  normalize_facets_depth(filename)
}

I made the following change to get it to work

$ git diff
diff --git a/normDepth.R b/normDepth.R
index eddaa91..d5c7866 100755
--- a/normDepth.R
+++ b/normDepth.R
@@ -73,5 +73,5 @@ if(!interactive()){
   parser = ArgumentParser()
   parser$add_argument('-f', '--file', type='character', help='Filename of counts file to be normalized.')
   args=parser$parse_args()
-  normalize_facets_depth(filename)
+  normalize_facets_depth(args$file)
 }

reporter fixed that shit omg