#!/bin/bash
#SBATCH -t 48:00:00
#SBATCH --nodes=1 --ntasks-per-node=14
#SBATCH --mem=120Gb
#SBATCH --export=NONE
#SBATCH --mail-user=thpalma@uri.edu
#SBATCH --mail-type=END,FAIL

# Purge all previously loaded modules
module Purge

# Load SAMtools modules
module load SAMtools/1.9-foss-2018b

# Array of file paths
files=(TP1_trimmed/TP1_trimmed-mapped.sam TP2_trimmed/TP2_trimmed-mapped.sam TP3_trimmed/TP3_trimmed-mapped.sam)

for file in "${files[@]}"; do
  # Extract file name and folder name
  filename="$(basename "$file")"
  folder="$(dirname "$file")"

  # Convert .sam file to .bam file
  bam_file="$folder/${filename%.*}.bam"
  samtools view -bS "$file" > "$bam_file"

  # Sort .bam file
  sorted_bam_file="$folder/${filename%.*}.sorted.bam"
  samtools sort "$bam_file" -o "$sorted_bam_file"

  # Create bam index file
  samtools index "$sorted_bam_file"

  # Create IGV folder and move generated files inside
  mkdir "$folder/IGV_mapped"
  mv "$bam_file" "$folder/IGV_mapped"
  mv "$sorted_bam_file" "$folder/IGV_mapped"
  mv "$sorted_bam_file".bai "$folder/IGV_mapped"
done