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 " + echo "usage: generation.sh " 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"