I need to split my bed file into files with the same sequence length, but my original input file is not the whole chromosome, but a list of annotations with variable lengths and gaps between them. BedTools windowMaker will split the fragments into the requested windows size only if the original fragment is larger than the window, but in my case it does not work as I want.

For instance, suppose I have as an input the following:

chr1    0    90
chr1    149    200
chr1    249    300
chr1    310    510

And want a bed files with 100bp such as

File 1:

chr1    0     90
chr1   149  159

File 2:

chr1   159   200
chr1   249   300
chr1   310   318

And so on...

Or something like:

chr1    0     90     block1
chr1   149  159   block1
chr1   159   200  block2
chr1   249   300  block2
chr1   310   318  block2

Bedtools outputs this instead:

chr1    0    90
chr1    149    200
chr1    249    300
chr1    310    410
chr1    410    510

Is there a way to define the output based on sequence length instead of windows?