#!/bin/bash

if [ $# -ne 1 ]; then
  echo "Usage: $0 <input_gtf_file>"
  exit 1
fi

input_gtf="$1"
output_prefix="output"
sorted_gtf="${output_prefix}.sorted.gtf"
sorted_gtf_gz="${sorted_gtf}.gz"

module load htslib

# Sort the input GTF file
sort -k1,1 -k4,4n -s "$input_gtf" > "$sorted_gtf"

# Compress the sorted GTF file
bgzip -c "$sorted_gtf" > "$sorted_gtf_gz"

# Index the compressed GTF file
tabix "$sorted_gtf_gz"

# Remove intermediate files
rm "$sorted_gtf"
echo "done"