# This computes a reduced-dimension inverse of (G + I*theta)  
#Run as: julia PCIG.jl <filename score matrix> <filename for file containing 2*P*(1-P)> <no. of chromosomes> the filenames must be common to all chromsomes
infile1=ARGS[1];
rhofile=ARGS[2];
chroms=parse(Int64,ARGS[3]);
theta=parse(Float64,ARGS[4]);   #Scalar added to diagonal of the genomic relationship matrix to make it positive definite

Ct=[];
rho=0;
N=0;# i=1
for i=1:chroms;
	C=readdlm("$(infile1).$i"); # Read in score data of chr i from file
	N=size(C,1); #no. of animal
	rho=rho+sum(readdlm("$(rhofile).$i")); # Trick to make only a number
	if i==1;
		Ct=C;
	else
		Ct=[Ct C];
	end;
end;

invMatrix=inv(Ct'*Ct+eye(size(Ct,2))*rho*theta);
IG=(1/theta)*(eye(N)-Ct*invMatrix*Ct'); # Computes the inverse, reduced-dimension GRM from the score matrix
writedlm("IG.txt",IG,"\t")