# HG changeset patch
# User davidvanzessen
# Date 1447339597 18000
# Node ID d09b1bdfd3884bbcd1995268c579c2c897269c01
# Parent  099cc1254f74cfcd0fa6dad9a6f7849c2bf875ab
Uploaded

diff -r 099cc1254f74 -r d09b1bdfd388 merge_and_filter.r
--- a/merge_and_filter.r	Mon Nov 09 07:21:09 2015 -0500
+++ b/merge_and_filter.r	Thu Nov 12 09:46:37 2015 -0500
@@ -13,12 +13,12 @@
 functionality=args[10]
 unique_type=args[11]
 
-summ = read.table(summaryfile, header=T, sep="\t", fill=T, stringsAsFactors=F)
-sequences = read.table(sequencesfile, header=T, sep="\t", fill=T, stringsAsFactors=F)
-mutationanalysis = read.table(mutationanalysisfile, header=T, sep="\t", fill=T, stringsAsFactors=F)
-mutationstats = read.table(mutationstatsfile, header=T, sep="\t", fill=T, stringsAsFactors=F)
-hotspots = read.table(hotspotsfile, header=T, sep="\t", fill=T, stringsAsFactors=F)
-gene_identification = read.table(gene_identification_file, header=T, sep="\t", fill=T, stringsAsFactors=F)
+summ = read.table(summaryfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
+sequences = read.table(sequencesfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
+mutationanalysis = read.table(mutationanalysisfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
+mutationstats = read.table(mutationstatsfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
+hotspots = read.table(hotspotsfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
+gene_identification = read.table(gene_identification_file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
 
 if(method == "blastn"){
 	"qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore"