## PBS -q xl230g9q
## PBS -l select=1:ncpus=1:mem=10g
## PBS -l walltime=03:00:00
## PBS -l cput=30:00:00

source activate nn_Polina_tf2;
WORK_DIR=~/loxP_project/2022-06-14_rings/
cd $WORK_DIR;
[ -d stat ] || mkdir stat

declare -a files=("HAP8VIR_sub11" "HAP8VIR_sub17" "HAP8VIR_sub26" "HAP8VIR_sub30" "HAP8VIR_sub9" "HAP8VIR_sub14" "HAP8VIR_sub19" "HAP8VIR_sub27" "HAP8VIR_sub4" "HAP8VIR_sub15" "HAP8VIR_sub20" "HAP8VIR_sub28" "HAP8VIR_sub5" "HAP8VIR_sub16" "HAP8VIR_sub21" "HAP8VIR_sub29" "HAP8VIR_sub7" "undetermine")

for file in "${files[@]}"
do
echo ${file}
python ~/loxP_project/find_rearr_places.py ${WORK_DIR} ${file} $WORK_DIR/26_INS.txt $WORK_DIR/align/${file}/${file}.sorted.sam
done
