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Copy pathPlinkRead_binary2.m
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PlinkRead_binary2.m
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function genomat = PlinkRead_binary2(nsubj,snps,fileprefix)
persistent geno_values
% Written by Chun 2015
if ~issorted(snps), error('PlinkRead_binary2 expect sorted list of snps'); end;
nsnp = length(snps);
% bit shift to generate the genovalue matrix
bedprefix = sprintf('%s.bed', fileprefix);
%load('PlinkRead_binary2_geno_values.mat')
if isempty(geno_values)
geno_values = [
2 2 2 2
-1 2 2 2
1 2 2 2
0 2 2 2
2 -1 2 2
-1 -1 2 2
1 -1 2 2
0 -1 2 2
2 1 2 2
-1 1 2 2
1 1 2 2
0 1 2 2
2 0 2 2
-1 0 2 2
1 0 2 2
0 0 2 2
2 2 -1 2
-1 2 -1 2
1 2 -1 2
0 2 -1 2
2 -1 -1 2
-1 -1 -1 2
1 -1 -1 2
0 -1 -1 2
2 1 -1 2
-1 1 -1 2
1 1 -1 2
0 1 -1 2
2 0 -1 2
-1 0 -1 2
1 0 -1 2
0 0 -1 2
2 2 1 2
-1 2 1 2
1 2 1 2
0 2 1 2
2 -1 1 2
-1 -1 1 2
1 -1 1 2
0 -1 1 2
2 1 1 2
-1 1 1 2
1 1 1 2
0 1 1 2
2 0 1 2
-1 0 1 2
1 0 1 2
0 0 1 2
2 2 0 2
-1 2 0 2
1 2 0 2
0 2 0 2
2 -1 0 2
-1 -1 0 2
1 -1 0 2
0 -1 0 2
2 1 0 2
-1 1 0 2
1 1 0 2
0 1 0 2
2 0 0 2
-1 0 0 2
1 0 0 2
0 0 0 2
2 2 2 -1
-1 2 2 -1
1 2 2 -1
0 2 2 -1
2 -1 2 -1
-1 -1 2 -1
1 -1 2 -1
0 -1 2 -1
2 1 2 -1
-1 1 2 -1
1 1 2 -1
0 1 2 -1
2 0 2 -1
-1 0 2 -1
1 0 2 -1
0 0 2 -1
2 2 -1 -1
-1 2 -1 -1
1 2 -1 -1
0 2 -1 -1
2 -1 -1 -1
-1 -1 -1 -1
1 -1 -1 -1
0 -1 -1 -1
2 1 -1 -1
-1 1 -1 -1
1 1 -1 -1
0 1 -1 -1
2 0 -1 -1
-1 0 -1 -1
1 0 -1 -1
0 0 -1 -1
2 2 1 -1
-1 2 1 -1
1 2 1 -1
0 2 1 -1
2 -1 1 -1
-1 -1 1 -1
1 -1 1 -1
0 -1 1 -1
2 1 1 -1
-1 1 1 -1
1 1 1 -1
0 1 1 -1
2 0 1 -1
-1 0 1 -1
1 0 1 -1
0 0 1 -1
2 2 0 -1
-1 2 0 -1
1 2 0 -1
0 2 0 -1
2 -1 0 -1
-1 -1 0 -1
1 -1 0 -1
0 -1 0 -1
2 1 0 -1
-1 1 0 -1
1 1 0 -1
0 1 0 -1
2 0 0 -1
-1 0 0 -1
1 0 0 -1
0 0 0 -1
2 2 2 1
-1 2 2 1
1 2 2 1
0 2 2 1
2 -1 2 1
-1 -1 2 1
1 -1 2 1
0 -1 2 1
2 1 2 1
-1 1 2 1
1 1 2 1
0 1 2 1
2 0 2 1
-1 0 2 1
1 0 2 1
0 0 2 1
2 2 -1 1
-1 2 -1 1
1 2 -1 1
0 2 -1 1
2 -1 -1 1
-1 -1 -1 1
1 -1 -1 1
0 -1 -1 1
2 1 -1 1
-1 1 -1 1
1 1 -1 1
0 1 -1 1
2 0 -1 1
-1 0 -1 1
1 0 -1 1
0 0 -1 1
2 2 1 1
-1 2 1 1
1 2 1 1
0 2 1 1
2 -1 1 1
-1 -1 1 1
1 -1 1 1
0 -1 1 1
2 1 1 1
-1 1 1 1
1 1 1 1
0 1 1 1
2 0 1 1
-1 0 1 1
1 0 1 1
0 0 1 1
2 2 0 1
-1 2 0 1
1 2 0 1
0 2 0 1
2 -1 0 1
-1 -1 0 1
1 -1 0 1
0 -1 0 1
2 1 0 1
-1 1 0 1
1 1 0 1
0 1 0 1
2 0 0 1
-1 0 0 1
1 0 0 1
0 0 0 1
2 2 2 0
-1 2 2 0
1 2 2 0
0 2 2 0
2 -1 2 0
-1 -1 2 0
1 -1 2 0
0 -1 2 0
2 1 2 0
-1 1 2 0
1 1 2 0
0 1 2 0
2 0 2 0
-1 0 2 0
1 0 2 0
0 0 2 0
2 2 -1 0
-1 2 -1 0
1 2 -1 0
0 2 -1 0
2 -1 -1 0
-1 -1 -1 0
1 -1 -1 0
0 -1 -1 0
2 1 -1 0
-1 1 -1 0
1 1 -1 0
0 1 -1 0
2 0 -1 0
-1 0 -1 0
1 0 -1 0
0 0 -1 0
2 2 1 0
-1 2 1 0
1 2 1 0
0 2 1 0
2 -1 1 0
-1 -1 1 0
1 -1 1 0
0 -1 1 0
2 1 1 0
-1 1 1 0
1 1 1 0
0 1 1 0
2 0 1 0
-1 0 1 0
1 0 1 0
0 0 1 0
2 2 0 0
-1 2 0 0
1 2 0 0
0 2 0 0
2 -1 0 0
-1 -1 0 0
1 -1 0 0
0 -1 0 0
2 1 0 0
-1 1 0 0
1 1 0 0
0 1 0 0
2 0 0 0
-1 0 0 0
1 0 0 0
0 0 0 0
];
geno_values = cast(geno_values, 'int8');
end
if isempty(geno_values)
geno_values = zeros(256,4,'int8');
geno_code = [-1,1,0,2];
shiftind = [0,2,4,6];
indvec=zeros(1,4);
for i = 1:256;
ishift = int16(i-1);
for j = 1:4;
indvec(j) = bitand(bitsra(ishift,shiftind(j)),3) ;
end
indvec(indvec == 0) = 4;
geno_values(i,:) = geno_code(indvec);
end
%save('PlinkRead_binary2_geno_values.mat', '-v7', 'geno_values')
end
% Read in the binary file
bedid = fopen(bedprefix);
genobin = uint16(fread(bedid, 3));
% Check magic number
if genobin(1) ~= 108;
error('- Not a valid Plink BED file \r\n');
elseif genobin(2) ~= 27;
error('- Not a valid Plink BED file \r\n');
elseif genobin(3) ~= 1;
error('- Not in SNP-major format \r\n');
end
n_bytes = ceil(nsubj/4);
genomat = zeros(nsubj,nsnp,'int8');
for i = 1:nsnp;
fseek(bedid, 3 + (snps(i) - 1) * n_bytes, 'bof');
genobin = uint16(fread(bedid, n_bytes));
if length(genobin) ~= n_bytes, error('-- Invalid number of entries from the bed \r\n'); end
tmp_values = geno_values(genobin + 1, :)';
tmp_values = tmp_values(:);
genomat(:,i) = tmp_values(1:nsubj);
end
fclose(bedid);
end