Empty per-base output file if all reads in input BAM are unmapped about mosdepth HOT 5 CLOSED

thank you. I made a new release that incorporates this change.

from mosdepth.

Hi, per-base output is only reported for non-zero depth. This is by design.

from mosdepth.

Hi and many thanks for the quick reply! Could you please elaborate a little further on your comment?

When I run mosdepth on the following dummy SAM file

@HD	VN:1.6	SO:coordinate
@SQ	SN:ref	LN:47
seq	0	ref	10	60	38M	*	0	0	AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA	*	NM:i:0	MD:Z:38	AS:i:38	XS:i:0

I get this as per-base output:

$ zcat depth.per-base.bed.gz 
ref     0       9       0
ref     9       47      1

From your comment I wouldn't expect the first line to be there.

from mosdepth.

Hah, you got me. It's been a while since I really was deep into the mosdepth code.
Will you give this binary a try and let me know if it resolves your issue?

mosdepth_dev.gz

from mosdepth.

Nice, the binary gives the expected output (at least for the toy example above):

$ zcat depth_dev.per-base.bed.gz 
ref     0       47      0

from mosdepth.