hapsharing.m

function [hss] = hapsharing(s, pos)

% Population Genetics and Evolution Toolbox (PGEToolbox)
% Author: James Cai
% (c) Texas A&M University
%
% $LastChangedDate: 2013-01-06 13:39:38 -0600 (Sun, 06 Jan 2013) $
% $LastChangedRevision: 331 $
% $LastChangedBy: jcai $

%s=h1==h2;
if nargin < 2
    %   hss=zeros(1,length(h1));
    hss = zeros(size(s));
    st = sprintf('%d', s);
    [d1] = i_runscount(st, '0');
    [d0] = i_runscount(st, '1');
    leadingzerosn = 0;
    if ~s(1)
        leadingzerosn = d0(1);
        d0 = d0(2:end);
        hss = hss(leadingzerosn+1:end);
    end
    cd1 = cumsum(d1);
    cd0 = cumsum(d0);

    % need moving leading zeros
    if length(cd1) > length(cd0)
        idx = [0, cd1(1:end-1) + cd0] + 1;
        for k = 1:length(idx)
            hss(idx(k):idx(k)+d1(k)-1) = d1(k);
        end
    else % equal length
        idx = [0, cd1 + cd0] + 1;
        for k = 1:length(idx) - 1
            hss(idx(k):idx(k)+d1(k)-1) = d1(k);
        end
    end
    if leadingzerosn > 0
        hss = [zeros(1, leadingzerosn), hss];
    end
else
    hss = 0;
    if s(pos)
        s1 = s(1:pos-1);
        s1 = s1(end:-1:1);
        s2 = s(pos+1:end);
        [n1] = i_getn(s1);
        [n2] = i_getn(s2);
        hss = n1 + n2 + 1;
        hss = hss - (hss == 1);
    end
end


    function [n1] = i_getn(s1)
        n1 = 0;
        if ~isempty(s1) && s1(1)
            s1 = sprintf('%d', s1);
            t1 = textscan(s1, '%s', 'delimiter', '0', 'multipleDelimsAsOne', true);
            t1 = t1{:};
            n1 = length(t1{1});
        end

            function [d1] = i_runscount(st, delim)
                t1 = textscan(st, '%s', 'delimiter', delim, 'multipleDelimsAsOne', true);
                t1 = t1{:};
                d1 = zeros(1, length(t1));
                for k = 1:length(t1)
                    d1(k) = length(t1{k});
                end