Fix compile issues



See merge request !352

Feature small rna

smallRNA pipeline TinyCap

closes #237 
closes #258 
closes #265 
includes fixes for !306

See merge request !312

Seqstat: length array was too short for keeping the readlengths.

the array was too short

See merge request !349

Feature carp docs 0.6.0



See merge request !350

Fixed biopet logging

Fixes #293 

See merge request !351

Feature mergesvcalls

This branch will introduce the SV-merging tool for the VCF files generated by SV-callers in the ShivaSVcalling pipeline.

We now use the PySVtools made by @wyleung 

closes #236

See merge request !301

Feature toucan summary



See merge request !338

Fixed default value

Fixes #294 

See merge request !347

Feature docs 0.6.0

TODO:

- [x] ***Gears*** pipeline needs an example config
- [x] ***Gentrap*** refactored
- [ ] ***Toucan*** needs an disclaimer: When used with the Varda Db it assumes 2 vcf files as input
- [ ] ***Shiva*** add reference_fa to Required settings (maybe in all pipelines)
- [ ] ***Shiva*** add all variantcallers to the list of available variantcallers
- [ ] ***Shiva*** explain about public / private version of Shiva
- [ ] ***ShivaSVCalling*** 
- [ ] ***TinyCap*** add new documentation about the smallRNA pipeline.
- [x] ***Developer docs*** solves #261 - missing paragraph about the config and example code to implement using of the `config` in extensions/pipelines


Fixes #261 and #264

See merge request !315

Add all project VCF file merge into 1 global merge file

Branch for adding tests to increase test coverage for tools and utils



See merge request !332