Currently, our assembly.impute_from_reference command requires inFasta and inReference to have the same number of sequences. This is because, in order to perform imputation, we pairwise align the whole segment of inFasta segment i to inReference segment i because we don't want to guess which segment is which if we don't receive a complete genome.
But maybe in the case that inFasta has less than the full number of segments compared to inReference, the user is a bit desperate anyway.. maybe we can use skani to pick which inReference segment corresponds to which inFasta segment and proceed as before.
Currently, our
assembly.impute_from_referencecommand requiresinFastaandinReferenceto have the same number of sequences. This is because, in order to perform imputation, we pairwise align the whole segment of inFasta segment i to inReference segment i because we don't want to guess which segment is which if we don't receive a complete genome.But maybe in the case that
inFastahas less than the full number of segments compared toinReference, the user is a bit desperate anyway.. maybe we can use skani to pick whichinReferencesegment corresponds to whichinFastasegment and proceed as before.