BEGIN { OFS="\t" }

# Pass 1: Load Method A BED (gene body window)
FILENAME == methodA {
    key = $1 "," $2 "," $3
    geneA[key] = $4
    next
}

# Pass 2: Load Method B BED (nearest TSS)
FILENAME == methodB {
    key = $1 "," $2 "," $3
    geneB[key] = $4
    distB[key] = $5
    next
}

# Pass 3: Annotate OCR_allTissue.txt
FILENAME == mainfile {
    if (FNR == 1) {
        print $0, "Gene_bodyWindow_1Mb", "Nearest_TSS_1Mb", "Dist_to_TSS"
    } else {
        key = $1
        gA = (key in geneA) ? geneA[key] : "."
        gB = (key in geneB) ? geneB[key] : "."
        dB = (key in distB) ? distB[key] : "."
        print $0, gA, gB, dB
    }
}