From f4a001f821a8dfb310ea101051d7640d21a42ec1 Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Wed, 10 Mar 2021 12:33:25 +0100
Subject: [PATCH] Change CuReSim output file extension to FASTQ

---
 .gitignore    | 1 +
 generation.sh | 6 ++++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 2447fda..919f14d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 *.txt
 *.fasta
+*.fastq
diff --git a/generation.sh b/generation.sh
index 4b7292a..7e6a7e1 100755
--- a/generation.sh
+++ b/generation.sh
@@ -14,8 +14,10 @@ sequencing_runs=$2
 read_mean_size=350
 read_variance_size=0.0
 data_directory="data/"
-file="sequence.fasta"
+fasta=".fasta"
+fastq=".fastq"
+filename="sequence"
 prefix="curesim_"
 
 Rscript src/repertoire.r "$sequences" "$sequencing_runs"
-java -jar tools/CuReSim.jar -m "$read_mean_size" -sd "$read_variance_size" -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$filename$fasta" -o "$data_directory$prefix$filename$fastq"