From deb1066982e0ba83b77fdc1abac44a7def0366cf Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Tue, 2 Mar 2021 20:07:05 +0100
Subject: [PATCH] Set CuReSim read size to 350 bases

---
 generation.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/generation.sh b/generation.sh
index af20f37..4b7292a 100755
--- a/generation.sh
+++ b/generation.sh
@@ -11,9 +11,11 @@ fi
 
 sequences=$1
 sequencing_runs=$2
+read_mean_size=350
+read_variance_size=0.0
 data_directory="data/"
-file="sequence.fastq"
+file="sequence.fasta"
 prefix="curesim_"
 
 Rscript src/repertoire.r "$sequences" "$sequencing_runs"
-java -jar tools/CuReSim.jar -f "$data_directory$file" -o "$data_directory$prefix$file"
+java -jar tools/CuReSim.jar -m "$read_mean_size" -sd "$read_variance_size" -f "$data_directory$file" -o "$data_directory$prefix$file"