pybedtools
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Bad `all_hits` overlap result
Somehow, when the coordinates are big enough, all_hits produce wrong results:
bt1 = pybedtools.BedTool("chr1 50000001 50000002", from_string=True)
print(bt1.all_hits(pybedtools.Interval("chr1", 50000000, 50000001), overlap=1.0))
produces:
[Interval(chr1:50000001-50000002)]