Due to adding black as a precommit hook before starting work on this, there appears to be a lot of changes... Most of these are styling changes. Actual feature changes are mostly line 1003 of gnomonicus/gnomonicus_lib.py onwards
This adds FASTA file adjudication to prediction calling. There are cases in which clockwork will produce a FASTA file of mostly N values, but may have some entries in the minos VCF - resulting in a situation where bases called in the VCF may not correlate to the FASTA file. This should apply null rules from a catalogue if the FASTA file calls N values (as if they were in the VCF as ./. calls)
Due to adding black as a precommit hook before starting work on this, there appears to be a lot of changes... Most of these are styling changes. Actual feature changes are mostly line 1003 of
gnomonicus/gnomonicus_lib.pyonwardsThis adds FASTA file adjudication to prediction calling. There are cases in which
clockworkwill produce a FASTA file of mostlyNvalues, but may have some entries in the minos VCF - resulting in a situation where bases called in the VCF may not correlate to the FASTA file. This should apply null rules from a catalogue if the FASTA file callsNvalues (as if they were in the VCF as./.calls)