i believe there is an issue with make windows tool: i am attempting to create sliding windows on a set of intervals, however some valid windows seem to get tossed from final output as offset increases.
example input interval: chr1 0 681
example window, 120bp, offset 120bp: in this case I get the expected result chr1 0 120 chr1 120 240 chr1 240 360 chr1 360 480 chr1 480 600
example 120bp window, 240bp offset, result:
chr1 0 120 chr1 240 360
this is not what I would expect because the below interval is still valid, as output in first example. The offset and window size are still within the input boundary
chr1 480 600
example 120bp window, 360bp offset:
chr1 0 120
again now TWO valid intervals are rejected. I have not found precise pattern yet, however I see the issue in multiple datasets and occurs as the offset size approaches twice the window size. When windows are "end to end" or overlap the output is as expected.