`soft_exit_no_print(1)` returns 1 instead of 0 when calling help

Your default help messages return 1 as error code and the default is 0 for a good exit. Here is an example.

./snap-1.0beta.18/snap-aligner index --help
Welcome to SNAP version 1.0beta.18.
... 
$ echo $?
1
$ cat --help
...
$ echo $?
0

Possible solutions (pick whatever catches your fancy)

rewrite usage to take an exit code (usage_with_exit(0))
exit locally after calling usage()
wrap usage into two other subroutines one exits correctly with error code 0 and another exits with error code 1.
Think of a nice one!

One of the afflicting soft_exit_no_print(1) statements is present at :

amplab / snap