recombinant HCV genome not detected as such

[sschmutz]

Example 1000421130

despite there's a recombinant sequence (in case of HCV just one, HCV-1b/2k) which is very close to the actual sequence (created with SmaltAlign), MinVar chose a non recombinant sequence as reference:
in minvar.log INFO 2018/11/29 09:13:23 prepare.py: main() 472: Using non recombinant

This then leads to a cns_ambiguous.fasta sequence which contains a lot of Ns
The recombinant form is also not listed in subtype_evidence.csv

[MaryamZaheri]

The logic in MinVar is that if the viral reads are aligned to a non_recombinant reference more than 50% then do not try the recombinant reference sequences.