The following file is tolerated by GentNextBed(sorted=True). It is because the starts are checked but we don't keep track of which chroms have already been seen.
$ cat cluster.bed
chr1 10 20 a 1 +
chr1 25 30 b 2 +
chr1 25 35 c 3 +
chr1 27 33 d 4 -
chr2 27 31 e 5 -
chr1 50 80 f 6 +
chr1 51 81 g 7 -
# strandless clustering works fine:
$ clusterBed -i cluster.bed
chr1 10 20 a 1 + 1
chr1 25 30 b 2 + 2
chr1 25 35 c 3 + 2
chr1 27 33 d 4 - 2
chr2 27 31 e 5 - 3
chr1 50 80 f 6 + 4
chr1 51 81 g 7 - 4
The following file is tolerated by GentNextBed(sorted=True). It is because the starts are checked but we don't keep track of which chroms have already been seen.