fix default_lift_data

[mkanai]

The current default_lift_data doesn't work since new_locus is set as new_locus=lifted_over_locus.result in liftover_expr as below. This PR fixes this error.

gnomad_methods/gnomad/utils/liftover.py

Lines 95 to 103 in ef0fbf3

	return hl.struct(
	new_locus=lifted_over_locus.result,
	new_alleles=lifted_over_alleles,
	original_locus=locus,
	original_alleles=alleles,
	locus_fail_liftover=hl.is_missing(lifted_over_locus),
	ref_allele_mismatch=lifted_over_locus.result.sequence_context()
	!= lifted_over_alleles[0],
	)

[ch-kr]

thanks for catching this! LGTM.

I have two small comments -- could you reformat with black and add an entry to the changelog noting the fix?

[ch-kr]

ah sorry just saw this #269

[mkanai]

Thanks Katherine! I added the changelog.

[nawatts]

Hi @mkanai. The master branch has been repaired. If you update your branch, Pylint and documentation checks should run now.

[mkanai]

@nawatts thanks! I updated and it seems all checks have passed.