#!/bin/bash

bam_s3_bucket="quantgene-wes-archive"
upload_s3=true

file=${1--}

# --------------------- Download files from S3 -----------------------
while IFS= read vcf_s3; do
  temp=($(echo $vcf_s3 | tr "/" "\n"))
  vcf_s3_bucket="${temp[1]}"
  flowcell="${temp[2]}"
  run="${temp[3]}"
  sample="${temp[4]::-4}"
  
  vcf_s3_prefix="s3://${vcf_s3_bucket}/${flowcell}/${run}"
  bam_s3_prefix="s3://${bam_s3_bucket}/${run}"
  
  bam_s3="${bam_s3_prefix}/${sample}.deduped.bam"
  aws s3 cp $vcf_s3 data/
  aws s3 cp $bam_s3 data/
done < <(cat -- "$file")

# ------------------------ Index BAM files ---------------------------
for f in data/*.bam; do
  echo "Indexing: "$f
  samtools index $f $f".bai"
done