#!/bin/bash
set -euo pipefail

UNION="/BRC/yan/heart/adt_heart_narrowPeak/peak_union/all_peak_union.bed"
INDIR="/BRC/yan/heart/ATAC_heart_openbed"
OUTDIR="/BRC/yan/heart/ATAC_heart_openbed/counts"
mkdir -p ${OUTDIR}

# Step 1: count table per sample
for bed in ${INDIR}/step3.3_rmbl_Adule_*.open.bed; do
    sample=$(basename ${bed} .open.bed)
    out=${OUTDIR}/counts_${sample}.bed
    echo "[$(date)] ${sample}"
    bedtools coverage -a ${UNION} -b ${bed} -counts > ${out}
    echo "  → $(wc -l < ${out}) lines  →  ${out}"
done

# Step 2: merge into count matrix
echo "[$(date)] Merging into count matrix..."
paste ${OUTDIR}/counts_*.bed \
    | awk 'BEGIN{OFS="\t"} {
        printf $1"\t"$2"\t"$3;
        for(i=4; i<=NF; i+=4) printf "\t"$i;
        print ""
    }' > ${OUTDIR}/count_matrix.txt

echo "  → $(wc -l < ${OUTDIR}/count_matrix.txt) peaks  →  ${OUTDIR}/count_matrix.txt"
echo "[$(date)] Done."