# HG changeset patch
# User davidecangelosi
# Date 1559304565 14400
# Node ID f008adc272a2d16451a2fa368b26d413ae44e83c
# Parent  46cb147d53df57d629b018a8cc8d43c8a7b59c23
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit edd961b682ee4b19ba87eb7bd63ad169aa9678ea

diff -r 46cb147d53df -r f008adc272a2 pipe-t.R
--- a/pipe-t.R	Fri May 31 08:08:04 2019 -0400
+++ b/pipe-t.R	Fri May 31 08:09:25 2019 -0400
@@ -288,7 +288,7 @@
 .readCtCFX	<- function(readfile=readfile, n.data=n.data, i=i, nspots=nspots, ...)
 {
 	# Read data, skip the required lines
-	out	<- read.csv(file=readfile, header=TRUE, as.is=TRUE, nrows=nspots*n.data[i], strip.white=TRUE, ...)
+	out	<- read.delim(file=readfile, header=TRUE, as.is=TRUE, nrows=nspots*n.data[i], strip.white=TRUE, ...)
 	# Return
 	out
 } # .readCtCFX
@@ -297,7 +297,7 @@
 function(readfile=readfile, n.data=n.data, i=i, nspots=nspots, ...)
 {
 	# Read data
-	out	<- read.csv(file=readfile, header=TRUE, as.is=TRUE, nrows=nspots*n.data[i], strip.white=TRUE, ...)
+	out	<- read.delim(file=readfile, header=TRUE, as.is=TRUE, nrows=nspots*n.data[i], strip.white=TRUE, ...)
 	# Regard those marked as outliers as "Unreliable"
 	out$ThroughHole.Outlier[out$ThroughHole.Outlier=="False"]	<- "OK"
 	out$ThroughHole.Outlier[out$ThroughHole.Outlier=="True"]	<- "Unreliable"	
@@ -314,7 +314,7 @@
 	if (length(n.header)==0) 
 		n.header	<- 0
 	# Read data, skip the required lines
-	out	<- read.csv(file=readfile, header=TRUE, as.is=TRUE, nrows=nspots*n.data[i], skip=n.header, strip.white=TRUE, ...)
+	out	<- read.delim(file=readfile, header=TRUE, as.is=TRUE, nrows=nspots*n.data[i], skip=n.header, strip.white=TRUE, ...)
 	# Convert the calls into flags
 	out$Call[out$Call=="Pass"] <- "OK"
 	out$Call[out$Call=="Fail"] <- "Undetermined"