d4tools view - Flag `--region-file` not working.

[Pontus Höjer]

Hi,

I am trying to use d4tools view on my d4 file but don't get any output. I am using the command as below.

$ d4tools show --region-file tmp.bed DBS_MM+SM.mosdepth.per-base.chr1.d4 | head

This is the head of the d4 file.

$ d4tools show DBS_MM+SM.mosdepth.per-base.chr1.d4 | head
chr1	0	9997	0
chr1	9997	9998	1
chr1	9998	9999	4
chr1	9999	10000	6
chr1	10000	10001	541
chr1	10001	10002	549
chr1	10002	10003	571
chr1	10003	10004	731
chr1	10004	10005	752
chr1	10005	10007	810

and this is the top of the BED regions.

$ head tmp.bed 
chr1	10000	11014
chr1	11031	11058
chr1	11079	11453
chr1	15792	15854
chr1	16707	16749
chr1	19300	19448
chr1	20823	20868
chr1	26448	26470
chr1	29739	29797

From this I would have expected the output when using --region-file

$ d4tools show --region-file tmp.bed DBS_MM+SM.mosdepth.per-base.chr1.d4 | head

chr1	10000	10001	541
chr1	10001	10002	549
chr1	10002	10003	571
chr1	10003	10004	731
chr1	10004	10005	752
chr1	10005	10007	810
...

... but this is apparently not the case. Any ideas?

Install: Bioconda
Version: D4 Utilities Program 0.3.8(D4 library version: 0.3.7)