Hi,
This is more of a user error, but maybe a helpful bug to fix. This is on

samtools 1.19-1-ga4c73e4-dirty
Using htslib 1.19-1-g61b037bb-dirty

If I try to do something with a cram, but pass a non-existant reference (in this case a typo) samtools stats --reference <ref_with_typo> sample.cram, I get the following output that misleadingly suggests the cram file itself doesn't exist.

[E::refs_load_fai] Failed to open reference file '<ref_with_typo>'
[E::hts_open_format] Failed to open file "sample.cram" : No such file or directory
samtools stats: failed to open "sample.cram": No such file or directory

Oddly, in the case of stats I get a segfault, but in other operations like view I just get the errors that the reference can't be opened and the cram doesn't exist. I would guess the expected behaviour would be error out when the reference couldn't be loaded and avoid misleading the user the cram file doesn't exist (and potentially segfault).

Best,
Alex