calculating af_or using function and cmd options now

scripts/functions/myaf_or_calcs.R

@@ -1,15 +1,16 @@
-my_afor <- function (  infile_master
+my_afor <- function (  drug
+                     , gene
+                     , infile_master
                      , infile_metadata
                      , outfile
-                     , drug
-                     , gene
-                     , idcol = "id"
+                     , idcol
                      , dr_muts_col
                      , other_muts_col){
 
   #===========================================
   # 1: Read master/raw data stored in Data/
   #===========================================
+  cat(infile_master)
   raw_data_all = read.csv(infile_master, stringsAsFactors = F)
   
   cat("\nExtracting columns based on variables:\n"