Fix bug where processDefaultValues reads past the first '='

[Wytamma]

If traits defaults are specified by the user in the form value="$(dateTrait.value=68BO_2011.0=2011.0,65BO_2013.0=2013.0,97SGR_2012.0=2012.0..." BEAST would read past the first '=' to the last '='. This makes the parserDefinitions key equal "dateTrait.value=68BO_2011.0=2011.0,65BO_2013.0=2013.0,97SGR_2012.0" and value "2012.0". I fixed this by only setting k to the index of the first '='.

[Wytamma]

Sorry! I made a typo in the only change I made (facepalm). Have now fixed.

[rbouckaert]

Interesting way to use defaults.

[Wytamma]

Thanks for accepting my PR! I made a small library for creating dynamic BEAST XML files so that all parameters can be set at runtime https://github.com/Wytamma/dynamic-beast. Cheers!

[rbouckaert]

Thanks for the link. Judging from the example (dynamic_BEAST.xml) I noticed that partition information gets removed (in order to prevent clutter in online defintiions?), and wonder how it works when there are multiple partitions. Say, there are two partitions, both with gammaCategoryCount=4 by default. Will running BEAST with -D SiteModel.gammaCategoryCount=8 change the category count of both partitions, or will partition information be added in this instance and category counts remain 4?

[Wytamma]

Ah! Yeah you're right! I've updated it now so that you have to specify the full path e.g. beast -D 'clockRate.c:hcv=7.9E-4' dynamic_hcv_coal.xml. No as clean of an interface but the only way it'll work I guess. Thanks for the input on yet another way to generate a BEAST XML file 😂