Daniel Danis

Hello @glustein I think the following line is the culprit: ``` org.h2.jdbc.JdbcSQLNonTransientConnectionException: A file path that is implicitly relative to the current working directory is not allowed in the database...

Where is your data folder?

[This](https://exomiser.readthedocs.io/en/latest/installation.html#configuring-the-application-properties) can be helpful.

Hi, thanks for the explanation, this is useful for both prongs of my question! After a second thought, I agree that a reference range, if present, should have both bounds....

An example to demonstrate the mishap (can be used in `ProtoParserTest`): This code parsers the above phenopacket: ```java @Test void readV1PhenopacketJson() { // Path to the phenopacket from Mike's post...

It is possible to implement "sniffing" - determine the format (YAML, JSON, or Protobuf) and the top-level element, at least to some extent. A simple strategy can test if the...

@pnrobinson yeah, the sniffing is turned off if the user is explicit with the input using `-f | --format` or `-e | --element` CLI options.

I wonder if you would find it useful to allow sorting the phenotypic features in the output, e.g. to put the more similar features together. In principle, something like [hierarchical...

Hi @cmungall yes, these are good points. > in general you don't distribute top level namespaces alongside your own. Occasionally when vendoring is really necessary it's made a sub-namespace I...

Hi @monicacecilia it is understood that the updates must be discussed in the manner you outlined. This PR makes _no_ backward incompatible changes - everything that worked in `v2.0.2` or...