Closed philipwfowler closed 1 year ago
Is this on the main
branch or large-deletions
?
main
for both
This is also cropping up in the foo.mutations.csv
table where MUTATION
is e.g. S450S
rather than rpoB@S450S
or having gene separately specified
With the latest main
branch of both gumpy
and gnomonicus
, I can't reproduce either issue...
In effects.csv
I get NC_000962_3_test_0002,gyrA,A90V:0.05,test_001,MXF,U
which matches the 5% FRS in the VCF, which is <10% required for R
in the catalogue, so is a default rule match
In mutations.csv
, the gene is specified by the GENE
column - the columns are in a different order (not sure why) but the GENE
column definitely still exists. For my test, it was col 18
Having merged in large-deletions
this works as expected now, thanks. Closing.
If I pass a (i) VCF file with a minor population e.g. a row like
and call
gnomonicus
with a catalogue with an appropriate row e.g.NC_000962.3,test_001,v1.00,GARC1,RFUS,MXF,gyrA@A90V:0.1,R,{},{},{}
and supply a text file to
--minor_populations
containing 7570 then it complains asI put two
print
commands in and it seems thatdiff.minor_populations
is returningA90V:5
rather than the expectedgyrA@A90V
. This is therefore probably agumpy
bug but I am recording here. test_002.tgz