Are you using the latest version of samtools and HTSlib?

Using latest release

Please describe your environment.

Linux with gcc 8.2

Please specify the steps taken to generate the issue, the command you are running and the relevant output.

Running samtools cat -@ 4 file1.bam file2.bam fails with

cat: invalid option -- '@'
Segmentation fault

Running samtools cat --threads 4 file1.bam file2.bam is valid, and behaves as expected with multithreading.

Both options (@/threads) are specified in the documentation for samtools cat, and follows the notation for other tools, so hopefully a simple fix.