gumpy doesn't check that the `REF` field in a vcf file matches what it is the `Genome` object when adding
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philipwfowler commented
I can change the base in the REF
field and gumpy
doesn't complain. Since these are all the forward strand it should be easy to assert that the specified REF
base from a vcf file matches a Genome
object when you do
sample = reference + vcf
There will be a performance cost but I think it is worth it. Would automatically stop you trying to add two vcfs in succession both of which mutate the same base since after the first vcf it would not longer match REF
.
philipwfowler commented
Also worth checking that REF != ALT
in a vcf file --> in my testing files I managed to have an incorrect REF with a different ALT but the ALT matched the real REF so gumpy
produced no output which confused me for a while! These two rules would prevent that.