bin not yielding all windows

[gevro]

Hi,
There's some issue with bin. It is not producing bins for regions without data in the wiggle file, even after doing fillIn.
Instead it is just making a large bin with score = 0. But I want 100 bp bins regardless of whether there is data. And fillIn should work.

$ head -n 20 blah.windows.bg
chr1	0	100	0
chr1	100	200	0
chr1	200	300	0
chr1	300	400	0
chr1	400	500	0
chr1	500	600	0
chr1	600	700	0
chr1	700	800	0
chr1	800	900	0
chr1	900	1000	0
chr1	1000	1100	0
chr1	1100	1200	0
chr1	1200	1300	0
chr1	1300	1400	0
chr1	1400	1500	0
chr1	1500	1600	0
chr1	1600	1700	0
chr1	1700	1800	0
chr1	1800	1900	0
chr1	1900	2000	0

$ wiggletools write_bg - bin 100 scale 0.01 fillIn blah.windows.bg k24.umap.sorted.bw | head
chr1	0	100	0.137970
chr1	100	200	0.702080
chr1	200	300	0.210000
chr1	300	1800	0.000000
chr1	1800	1900	0.079950
chr1	1900	2300	0.000000
chr1	2300	2400	0.149580
chr1	2400	2500	0.180420
chr1	2500	2600	0.220080
chr1	2600	2800	0.000000

As you can see, there is an entry "chr1 300 1800 0.000000".
But the expected behavior should be as below, or at least an option to do that.
chr1 300 400 0.0000
chr1 400 500 0.0000
chr1 500 600 0.0000
...

[dzerbino]

Hello @gevro ,

This is because the bedgraph writer was trying to be too clever, and shared a compression module with the wiggle writer.

I have now deactivated this behaviour.

Cheers,

Daniel