Assign_barcodes.m

%% generate HW4 barcode
barcodes = GenerateExtendedHammingWords(18);%This function is from https://github.com/ZhuangLab/MERFISH_analysis
barcodes = barcodes(sum(barcodes,2)==4,:); 
[~,~,all]=xlsread(''); % Codebook path, first column is sorted by Chromosome
chr=[];
for i=1:length(all)
    temp=strfind(all{i,1},'.');
    chr(i)=str2num(all{i,1}(4:temp(1)));
end
%%
finalbarcodes=[];
finalbad=100;
for i=1:1000000 % randomly assign barcode to each loci until the barcode arrangement fit the criteria 
        barcodes = barcodes(randperm(size(barcodes,1)),:);
        accept=1;
        bad=0;
        for j=1:23
           idx=chr==j;
           tempcode=sum(barcodes(idx,:));
           if  sum(tempcode>5)>0
               accept=0;
               break;
           end
           if sum(tempcode>4)>0
               bad=bad+1;               
           end
        end
        
        if accept && bad<finalbad
            finalbarcodes=barcodes;
            finalbad=bad;
        end
end
%
for j=1:23
           idx=chr==j;
           tempcode=sum(finalbarcodes(idx,:));
           disp( ['Chr:' num2str(j)]);
           disp(tempcode);
           
end


disp(finalbarcodes)
% finalbarcodes is the barcode set for library design