REF=/data/Schwartz/brentp/mm10/ref/mm10.fa
BIS_REF=$(dirname $REF)

PICARD=/home/brentp/src/picard/picard-tools-1.98
BSMOOTH=/home/brentp/src/bsmooth-align/

TEMP=/scratch/brentp/

module load bsmap
module load bison/0.3.0

PATH=$PATH:~/src/sherman/

set -eo pipefail

name=real
name=sim


FQ1=data/${name}_R1.fastq.gz
FQ2=${FQ1/_R1/_R2}


TRIM_FQ1=${FQ1/.fastq/.trim.fastq}
TRIM_FQ2=${FQ2/.fastq/.trim.fastq}

OUT=results/


mkdir -p $OUT/trim/ logs/ data/

#if [ ! -e $TRIM_FQ1 ]; then
#    exit 1
#fi