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custom.lua
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function mean(vals)
local sum=0
for i=1,#vals do
sum = sum + vals[i]
end
return sum / #vals
end
function loc(chrom, start, stop)
return chrom .. ":" .. start .. "-" .. stop
end
CLINVAR_LOOKUP = {}
CLINVAR_LOOKUP['0'] = 'unknown'
CLINVAR_LOOKUP['1'] = 'germline'
CLINVAR_LOOKUP['2'] = 'somatic'
CLINVAR_LOOKUP['4'] = 'inherited'
CLINVAR_LOOKUP['8'] = 'paternal'
CLINVAR_LOOKUP['16'] = 'maternal'
CLINVAR_LOOKUP['32'] = 'de-novo'
CLINVAR_LOOKUP['64'] = 'biparental'
CLINVAR_LOOKUP['128'] = 'uniparental'
CLINVAR_LOOKUP['256'] = 'not-tested'
CLINVAR_LOOKUP['512'] = 'tested-inconclusive'
CLINVAR_LOOKUP['1073741824'] = 'other'
CLINVAR_SIG = {}
CLINVAR_SIG['0'] = 'uncertain'
CLINVAR_SIG['1�
8000
39;] = '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
-- from lua-users wiki
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
function contains(str, tok)
return string.find(str, tok) ~= nil
end
function div2(a, b)
if(a == 0) then return "0.0" end
return string.format("%.9f", (a + 0) / b)
end
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 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] = join(inret, "|")
end
end
return join(ret, ",")
end
join = table.concat
function check_clinvar_aaf(clinvar_sig, max_aaf_all, aaf_cutoff)
-- didn't find an aaf for this so can't be common
if max_aaf_all == nil or clinvar_sig == nil then
return false
end
if type(clinvar_sig) ~= "string" then
clinvar_sig = join(clinvar_sig, ",")
end
if false == contains(clinvar_sig, "pathogenic") then
return false
end
if type(max_aaf_all) ~= "table" then
return max_aaf_all > aaf_cutoff
end
for i, aaf in pairs(max_aaf_all) do
if aaf > aaf_cutoff then
return true
end
end
return false
end
function setid(...)
local t = {...}
local res = {}
local seen = {}
for i, v in pairs(t) do
if v ~= "." and v ~= nil and v ~= "" then
if seen[v] == nil then
res[#res+1] = string.gsub(v, ",", ";")
seen[v] = true
end
end
end
return table.concat(res, ";")
end