Added a better error handling on a missing reference.

Small change to better track missing references

See merge request !210

Issue186

See #186. 

See merge request !209

Changed dependency



See merge request !208

Ended up using HTSJDK nomenclature for genotype types
I.e: HET, HOM_REF, HOM_VAR, MIXED, NO_CALL and UNAVAILABLE

Upgrade shade plugin version



See merge request !207

Review kraken / gears



See merge request !205

Fix for #184

Fix for #184

See merge request !206

Feature upgrade queue 3.4

see also #175

See merge request !203

Feature add toucan to shiva

see also #176 and #182 and #183

See merge request !204