In BED format, start is zero-based, so a single nucleotide would have start 1 less than end. Furthermore, in a zero-based, half-open coordinate system, start==end indicates an insertion between nucleotides.
https://www.biostars.org/p/84686/
Therefore, the flanking nucleotides are affected. Thus, merge updates the start to reflect that the merger of the two intervals includes that flanking nucleotide.
Aaron
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