samtools quiet mode?

[g_solid]

Hi all,
I'm wondering if samtools has a quiet (silent) mode, where all output is suppressed. I couldn't locate such an option. It appears that, even if there are no errors, samtools output may be treated as an error message by other programs.
Your feedback on this would be appreciated.
Thanks

[drio]

Can you show us an example? What do you mean the output is treated as an error message by other programs?

Assuming you can redirect the stdout and stderr to different files. Also, checkout the return code from samtools (This is assuming you are in a UNIX environment using
a bash as a shell):

$ ./samtools <cmd> > ./stdout 2> ./stderr && echo $?

Anything other than 0 would indicate samtools failed while processing.

[g_solid]

Thanks for your suggestion. It may indeed be preferable to deal with the issue at the Unix level.
An example of the issue I was referring to is a "samtools view" command (to convert SAM to BAM): my command works correctly, as far as I can see, but also returns internal samtools messages that appear like errors, e.g. "[samopen] SAM header is present: 25 sequences."

[jmarshall]

Anything other than 0 would indicate samtools failed while processing.

I think you will find that samtools does not reliably set its exit status usefully. For example (with the current 0.1.8):

$ samtools view nonexistent.bam; echo "exit status: $?"
open: No such file or directory
[main_samview] fail to open file for reading.
exit status: 0