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function ratio(vals)
vals = vals[1] -- get 2 values per element. ref and alt counts.
if vals[2] == 0 then return "0.0" end
return string.format("%.9f", vals[2] / (vals[1] + vals[2]))
end
function contains(str, tok)
return string.find(str, tok) ~= nil
end
function split(str, sep)
local sep, fields = sep or ":", {}
local pattern = string.format("([^%s]+)", sep)
str:gsub(pattern, function(c) fields[#fields+1] = c end)
return fields
end
CLINVAR_SIG = {}
CLINVAR_SIG['0'] = 'uncertain'
CLINVAR_SIG['1'] = 'not-provided'
CLINVAR_SIG['2'] = 'benign'
CLINVAR_SIG['3'] = 'likely-benign'
CLINVAR_SIG['4'] = 'likely-pathogenic'
CLINVAR_SIG['5'] = 'pathogenic'
CLINVAR_SIG['6'] = 'drug-response'
CLINVAR_SIG['7'] = 'histocompatibility'
CLINVAR_SIG['255'] = 'other'
CLINVAR_SIG['.'] = '.'
function intotbl(ud)
local tbl = {}
for i=1,#ud do
tbl[i] = ud[i]
end
return tbl
end
function clinvar_sig(vals)
local t = type(vals)
-- just a single-value
if(t == "string" or t == "number") and not contains(vals, "|") then
return CLINVAR_SIG[vals]
elseif t ~= "table" then
if not contains(t, "userdata") then
if t == "string" then
vals = split(vals, ",")
else
vals = {vals}
end
else
vals = intotbl(vals)
end
end
local ret = {}
for i=1,#vals do
if not contains(vals[i], "|") then
ret[#ret+1] = CLINVAR_SIG[vals[i]]
else
local invals = split(vals[i], "|")
local inret = {}
for j=1,#invals do inret[#inret+1] = CLINVAR_SIG[invals[j]]
end
ret[#ret+1] = table.concat(inret, "|")
end
end
return table.concat(ret, ",")
end
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