Release 0.0.4 Notes

Behaviour changes

Aln2type will now take the requires option included in variant definitions, including chains of required definitions (i.e. variants that require a variant call which itself requires another variant call).
Two columns have been added to the sample summary CSV output: prelim_status and met_required which are both used to inform the new behaviour of the status column.
prelim_status only uses the mutations in the variant definition for a given call and does not refer to required variant calls (this is the same behaviour as the status column before this update).
met_required refers to whether or not a sample has probable or confirmed calls for all required variants - this includes any nested chains of required variants .
met_required returns nothing if the variant definition does not have any required calls; TRUE if the sample has confirmed or probable calls for all required variants, or FALSE if any required variant calls are missing or not confirmed or probable.
status will inherit the value of prelim_status if there are no required variants or if met_required is TRUE; if met_required is FALSE status will be low-qc.
The sample summary CSV continues to have a line for each variant call.