Are you using the latest version of samtools and HTSlib? If not, please specify.

(run samtools --version)

tested in 1.17

Please describe your environment.

• OS (run uname -sr on Linux/Mac OS or wmic os get Caption, Version on Windows)
• machine architecture (run uname -m on Linux/Mac OS or wmic os get OSArchitecture on Windows)
• compiler (run gcc --version or clang --version)

samtools on MingW installed with pacman (MingW package manger) - running on Windows.

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

When entering an invalid command line option, the software segfaults. This happens only on Windows, not Linux.

For example:
samtools.exe view --junk