#! /usr/bash
if [ "$#" -ne 5 ]; then
    echo "Usage: $0 <reference_genome> <fastq_1> <fastq_2> <output_directory> <stem>"
    exit 1
fi
ref=$1
fq1=$2
fq2=$3
outdir=$4
stem=$5
mkdir -p "$outdir"
hisat -p 4 --dta -x "$ref" -1 "$fq1" -2 "$fq2" -S "${outdir}/${stem}.sam"
samtools view -b -@ 4 "${outdir}/${stem}.sam" | samtools sort -@ 4 -o "${outdir}/${stem}.sorted.bam" --write-index
rm "${outdir}/${stem}.sam"
echo "Mapping completed. Sorted BAM file is at ${outdir}/${stem}.sorted.bam"