Modified methylation_sites resource to point to a resource with merged methylation data with autosomes and sex chromosomes and updated transform_grch38_methylation accordingly.

[jkgoodrich]

This is to add the methylation data for sex chromosomes that Ruchit gave us.

The current file is located here: gs://gnomad/v4.1/constraint/resources/methylation_all.ht

If it looks good I will move it to the staging location.

The file was created like this:

from gnomad.resources.grch38.reference_data import methylation_sites

methyl_autosomes = methylation_sites.ht()
methyl_chrx_par = hl.read_table("gs://gnomad/v4.1/constraint/resources/methylation_chrX_par.ht")
methyl_chrx_nonpar = hl.read_table("gs://gnomad/v4.1/constraint/resources/methylation_chrX.ht")
methyl_chry_nonpar = hl.read_table("gs://gnomad/v4.1/constraint/resources/methylation_chrY.ht")

methyl_chrx_par = methyl_chrx_par.rename({"methy_level": "methylation_level"}).select("methylation_level")
methyl_chrx_nonpar = methyl_chrx_nonpar.rename({"methy_level": "methylation_level"}).select("methylation_level")
methyl_chry_nonpar = methyl_chry_nonpar.rename({"methy_level": "methylation_level"}).select("methylation_level")

methyl_ht = methyl_autosomes.union(methyl_chrx_par, methyl_chrx_nonpar, methyl_chry_nonpar)
methyl_ht = methyl_ht.naive_coalesce(1000).checkpoint("gs://gnomad/v4.1/constraint/resources/methylation_all.ht", overwrite=True)

[ch-kr]

one minor comment