search

38 / d4-format

The D4 Quantitative Data Format
MIT License
156 stars 20 forks source link

d4tools view - Flag `--region-file` not working. #68

Open pontushojer opened 1 year ago

pontushojer commented 1 year ago

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)