Bug in normDepth.R
soccin opened this issue · 1 comments
soccin commented
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)
}
lordzappo commented
reporter fixed that shit omg