v0.0.4

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.