filterinfo.jl

# Basic julia script for filter INFO in VCF files

using BGZFStreams

# usage: julia filterinfo.jl input.vcf output.vcf INFO
sin = BGZFStream(ARGS[1])
sout = BGZFStream(ARGS[2],"w")
min_info = parse(Float64,ARGS[3]) 
min_maf = parse(Float64,ARGS[4])

println(string("IN:", ARGS[1]))
println(string("OUT:", ARGS[2]))
println(string("INFO:", ARGS[3]))
println(string("MAF:", ARGS[4]))

for line in eachline(sin)
	if occursin(r"^#", line)
		write(sout,line)
	else
		fields = split(line)
		info_field = fields[8]
		info_subfields = split(info_field,';')
        maf_ok = false
        info_ok = false
		for subfield in split(info_field,';')
			if occursin(r"^INFO=", subfield) || occursin(r"^R2=", subfield)
				if min_info < parse(Float64,(split(subfield,'=')[2]))
                    info_ok = true
				end
            elseif occursin(r"^MAF", subfield)
                if min_maf < parse(Float64,(split(subfield,'=')[2]))
                    maf_ok = true
                end
			end

		end
        info_ok && maf_ok && write(sout,line)
	end
end
		
close(sin)
close(sout)