trying `hts_nim_tools count-reads <bed> <bam>` only return 0 counts

[ipstone]

Do we need specific version hts-nim-tools to get this working? I use conda install -c conda-forge -c bioconda hts-nim-tools to install the hts-nim-tools.

My bed files are in the folllowing format:

chr5    38702540        38722603
chr12   98136449        98156541
chr8    91644923        91665040
...

[brentp]

does your bam file have chromosomes with the "chr" prefix?

[smoe]

Please allow a quick sidetrack since this issue has the culprit in its title. I have just prepared the Debian package for hts-nim-tools and interpreted the .nimble build instructions on https://github.com/brentp/hts-nim-tools/blob/f03225bd9a9273c1a0b3711fd5e73cf1c81e778b/hts_nim_tools.nimble#L15 as a clear indication that the executable should be hts-nim-tools, not hts_nim_tools.

Is my interpretation correct?

[brentp]

it does, but it's probably better to name it hts_nim_tools. I can change this if it simplifies things.

[smoe]

Hm. I might want to come back to that but for the moment - let's see where this carries us. I just added a symlink so either variant is fine. And, while I have not yet completely thought this through, I would like to leave this as a simple vivid use case for Debian's interaction with bio.tools and SciCrunch - @joncison, @hmenanger, @matuskalas - can I drag you into this thread this way? Any opinion of yours?