#!/usr/bin/env bash
set -euo pipefail

indir="/BLUES/eric/ONT/MAPQ_bam"
cd "$indir"

declare -A files=(
  [ONT_Naive]="ONT_Naive.MAPQ10.primary.5mC_CpG_combined.bed.gz"
  [ONT_Primed]="ONT_Primed.MAPQ10.primary.5mC_CpG_combined.bed.gz"
  [ONT_TSC]="ONT_TSC.MAPQ10.primary.5mC_CpG_combined.bed.gz"
)

for sample in "${!files[@]}"; do
  infile="${files[$sample]}"
  outfile="${sample}.MAPQ10.primary.onC.methylC.gz"

  echo "Converting $sample"
  echo "  input:  $infile"
  echo "  output: $outfile"

  zcat "$infile" \
    | awk 'BEGIN{OFS="\t"}
        /^track/ || /^browser/ || /^#/ {next}
        NF >= 11 {
          meth = $11 / 100;
          cov  = $10;
          print $1, $2, $3, "CG", meth, "+", cov
        }' \
    | gzip -c > "$outfile"
done

echo "Done:"
ls -lh *.MAPQ10.primary.onC.methylC.gz