#! /bin/bash
set -e
THREADS=${THREADS:-6}
if [ "$#" -ne 4 ]; then
    echo "Usage: $0 <reference_genome> <fastq_1> <fastq_2> <output_prefix>"
    exit 1
fi

ref=$1
fq1=$2
fq2=$3
out=$4
outdir=$(dirname "$out")
mkdir -p "$outdir"
hisat2 -p "$THREADS" --dta -x "$ref" -1 "$fq1" -2 "$fq2" -S "${out}.sam"
samtools view -b -@ "$THREADS" "${out}.sam" | samtools sort -@ "$THREADS" -o "${out}.sorted.bam" --write-index
rm "${out}.sam"
echo "Mapping completed. Sorted BAM file is at ${out}.sorted.bam"