bedtools2
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pairToBed ignores interval of length one
a.bedpe chr1 10 10 chr1 50 100 chr1 9 10 chr1 50 100
b.bed chr1 1 20
$ bedtools pairtobed -type either -a a.bedpe -b b.bed chr1 9 10 chr1 50 100 chr1 1 20