From f8c17ad83ad55a5f6492936fc367e87a3b3319dd Mon Sep 17 00:00:00 2001
From: mjko1210 <mjko1210@gmail.com>
Date: Fri, 2 Jul 2021 11:15:07 -0700
Subject: [PATCH] use fread instead of read.delim

---
 scripts/runIchorCNA.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/runIchorCNA.R b/scripts/runIchorCNA.R
index 61ab6cb..bf1be7e 100644
--- a/scripts/runIchorCNA.R
+++ b/scripts/runIchorCNA.R
@@ -73,6 +73,7 @@ library(GenomicRanges)
 library(GenomeInfoDb)
 library(foreach)
 library(doMC)
+library(data.table)
 options(stringsAsFactors=FALSE, bitmapType='cairo')
 
 patientID <- opt$id
@@ -152,7 +153,7 @@ if (substr(tumour_file,nchar(tumour_file)-2,nchar(tumour_file)) == "wig") {
 if (is.null(exons.bed) || exons.bed == "None" || exons.bed == "NULL"){
   targetedSequences <- NULL
 }else{
-  targetedSequences <- read.delim(exons.bed, header=T, sep="\t")  
+  targetedSequences <- fread(exons.bed)
 }
 
 ## load PoN