The STAR command is not very helpful. This will annoy potential users. Especially as the documentation is a PDF, and the src/ distribution doesn't even include it. An ASCII README for basic usage and some pointers to the documentation.

% STAR

EXITING because of fatal input ERROR: could not open readInFile=Read1

% STAR -h % STAR --help

EXITING: FATAL INPUT ERROR: empty value for paramter "-h" in input "Command-Line-Initial" SOLUTION: use non-empty value for this parameter

Thanks for this suggestion, I will include some help info in the next release.