From 2a997a3e5c2d254ccd44b70d993658897ad1a1ef Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Wed, 21 Apr 2021 20:09:02 +0200
Subject: [PATCH] Rename sequencing_runs to number_of_reads

---
 generation.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/generation.sh b/generation.sh
index eb61cdb..1bf9f3d 100755
--- a/generation.sh
+++ b/generation.sh
@@ -1,7 +1,7 @@
 #!/bin/sh
 
 usage() {
-	echo "usage: generation.sh <number of sequences> <sequencing runs>"
+	echo "usage: generation.sh <number of sequences> <number_of_reads>"
 	exit 1
 }
 
@@ -10,7 +10,7 @@ if [ $# != 2 ]; then
 fi
 
 sequences=$1
-sequencing_runs=$2
+number_of_reads=$2
 read_mean_size=350
 read_variance_size=0.0
 data_directory="data/"
@@ -19,5 +19,5 @@ fastq=".fastq"
 filename="sequence"
 prefix="curesim_"
 
-Rscript src/repertoire.r "$sequences" && java -jar tools/CuReSim.jar -n $((sequencing_runs * sequences)) -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"
+Rscript src/repertoire.r "$sequences" && java -jar tools/CuReSim.jar -n $((number_of_reads * sequences)) -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$filename$fasta" -o "$data_directory$prefix$filename$fastq"
 rm "$data_directory/log.txt"