Funcotator: Catch true variant problems and report all at end

[alanhoyle]

Feature request

Tool(s) or class(es) involved

Funcotator

Description

When running Funcotator on a large VCF, it can take several hours to complete, but each variant row is handled separately, row 1 and row 5 million are equally likely to have problems. Currently, a sufficiently malformed variant row causes it to crash and leave partial output.

It would be much friendlier if the true crash problems (e.g. something like "invalid interval") were saved and the crash-causing variant lines reported in bulk at completion, sending an OS exit code/error then.

It might even be a configurable option to exit immediately or save until end.

I do think it is appropriate to crash if a problem is encountered while parsing the header lines.