--- a/mutation_analysis.r	Wed May 04 04:28:02 2016 -0400
+++ b/mutation_analysis.r	Wed May 04 08:40:31 2016 -0400
@@ -6,7 +6,6 @@
 input = args[1]
 genes = unlist(strsplit(args[2], ","))
 outputdir = args[3]
-print(args[4])
 include_fr1 = ifelse(args[4] == "yes", T, F)
 setwd(outputdir)
 
@@ -28,8 +27,6 @@
   stop("No data")
 }
 
-
-
 cleanup_columns = c("FR1.IMGT.c.a",
                     "FR2.IMGT.g.t",
                     "CDR1.IMGT.Nb.of.nucleotides",
@@ -111,7 +108,7 @@
   dat[,col] = gsub("\\(.*\\)", "", dat[,col])
   #dat[dat[,col] == "",] = "0"
   dat[,col] = as.numeric(dat[,col])
-  dat[is.na(dat[,col]),] = 0
+  dat[is.na(dat[,col]),col] = 0
 }
 
 regions = c("FR1", "CDR1", "FR2", "CDR2", "FR3")
@@ -171,7 +168,6 @@
 
 setwd(outputdir)
 
-
 calculate_result = function(i, gene, dat, matrx, f, fname, name){
 	tmp = dat[grepl(paste(".*", gene, ".*", sep=""), dat$best_match),]
 
@@ -313,7 +309,6 @@
 	install.packages("ggplot2", repos="http://cran.xl-mirror.nl/") 
 }
 
-
 genesForPlot = gsub("[0-9]", "", dat$best_match)
 genesForPlot = data.frame(table(genesForPlot))
 colnames(genesForPlot) = c("Gene","Freq")
@@ -330,7 +325,6 @@
 pc
 dev.off()
 
-
 #blegh
 genesForPlot = dat[grepl("ca", dat$best_match),]$best_match
 if(length(genesForPlot) > 0){