The issue that arose was the -H is used for both homology group files and homology group identifiers according to the code.
However, the argument parsing assumed it always was a file.
We should therefore split the argument based on what it means.
I let -H be used for homology group files and -G for a list of homology groups.
Both are comma-separated still.
I also created an ArgGroup class for them being mutually exclusive.
NB: I introduced one unresolved issue: providing a string to -G gives a weird error message that I cannot handle with bean validation?
-
Fix weird error message with -Gand a non-integer input.
IMPORTANT: This is a merge request to the pantools_v3.5 branch, which will later on be merged into master.