Generic liftover

[lfrancioli]

Right now much of the code in utils.liftover is specific (or has specific options) for gnomad; specific parts should be moved to gnomad_qc.v2 and all there should be generic.

I also think that checkpointing should be taken out of e.g. lift_data since it may not be desirable in all situations (e.g very small table)

Finally, docstring needs work, e.g. :param rg: Reference genome --> is this the old or new reference?

[lfrancioli]

Something like this may be generally useful:

def liftover_expr(
        locus: hl.expr.LocusExpression,
        alleles: hl.expr.ArrayExpression,
        destination_ref: hl.ReferenceGenome
) -> hl.expr.StructExpression:

    lifted_over_locus=hl.liftover(locus, destination_ref, include_strand=True)
    lifted_over_alleles=alleles.map(
        lambda a: hl.if_else(lifted_over_locus.is_negative_strand,  hl.reverse_complement(a), a)
    )
    return hl.struct(
        locus=lifted_over_locus.result,
        alleles=lifted_over_alleles
    )

Also, something else to consider:

        bad_liftover=(
            hl.is_missing(lifted_over_locus) |
            (lifted_over_locus.sequence_context() != lifted_over_alleles[0][0])
        )

[nawatts]

Related to #162

[ch-kr]

Finally opened a PR for this: #246

[nawatts]

Now that #246 is merged, is this issue resolved?

[lfrancioli]

Yup!