Configuration

hgvs.config

The defaults are:

[mapping]
alt_aln_method = splign
assembly = GRCh38
in_par_assume = X
inferred_p_is_uncertain = True
normalize = True
prevalidation_level = EXTRINSIC
replace_reference = True

# strict_bounds: require transcript variants to be within transcript sequence bounds
strict_bounds = True

# add gene symbol: add gene symbol on converted variants
add_gene_symbol = False


[formatting]
max_ref_length = 0
p_3_letter = True
p_term_asterisk = False
p_init_met = True

[validator]
strict = True


[normalizer]
cross_boundaries = False
shuffle_direction = 3
validate = True
window_size = 20


[lru_cache]
maxsize = 100


[uta]
pooling = False
pool_min = 1
pool_max = 10

prd_uta_version = uta_20210129
stg_uta_version = uta_20210129
dev_uta_version = uta_20210129
public_host = uta.biocommons.org
local_host = localhost
public_prd = postgresql://anonymous:anonymous@${public_host}/uta/${prd_uta_version}
public_stg = postgresql://anonymous:anonymous@${public_host}/uta/${stg_uta_version}
public_dev = postgresql://anonymous:anonymous@${public_host}/uta_dev/${dev_uta_version}
local_prd  = postgresql://anonymous:anonymous@${local_host}/uta/${prd_uta_version}
local_stg  = postgresql://anonymous:anonymous@${local_host}/uta/${stg_uta_version}
local_dev  = postgresql://anonymous:anonymous@${local_host}/uta_dev/${dev_uta_version}