trying `hts_nim_tools count-reads <bed> <bam>` only return 0 counts about hts-nim-tools

[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

hts-nim-tools/hts_nim_tools.nimble

Line 15 in f03225b

exec "nimble c --out:bin/hts-nim-tools src/hts_nim_tools"

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?