GitLab

Make sure toucan creates bed track for varda based on all calls (including ref calls!), but only upload variants in vcf.
If we wouldn't do this, varda would show much higher frequencies than we actually want to show:
Varda calculates frequencies based on how many samples are covered at that position.

Fix shiva bcftools calling

- [x] Test bcftools
- [x] Add merge to bcftools singlesample
- [x] Test bcftools singlesample


See merge request !254

Fix sample names on VCFs used in by tool tests

 * Replaces identifiers (e.g. Child_something) with `Sample_101` etc. 
 * Some proper temp file creation for more tools 

See merge request !259

Fix typo of trait class ToolCommandFuntion -> ToolCommandFunction #221

Fixes #221 

See merge request !258

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

feature parralel mapping tests

This small improvement makes test for mapping 8x faster

See merge request !252