Fix typo of trait class ToolCommandFuntion -> ToolCommandFunction #221

Fixes #221 

See merge request !258

WIP

Update filename + extension retrieval in Flexiprep

Two changes:

* Refactored the uncompressed filename + extension retrieval. Also made sure now that extension trimming is case-insensitive (".gzip" and ".GZIP" are both trimmed).

* Added a clearer error message when the input file doesn't have any extension.

See merge request !256

Fixes #213

Quick fix for #213 

See merge request !249

Extracted version in a trait

Fixes #218 

See merge request !251

Fix memory test threads

Java did take a few Gb's for each threads, on a desktop you have not enough memory anymore. Fixed this to give those threads a memory limit.

See merge request !255