function [cast] = read_ocldb_write_mat(input_dir,filename,output_dir,inst)

%input_dir = '/home/eleanor/data/WOD/wod05/';
%filename = 'ocldb1169076334.845.CTD';
%output_dir = '/home/eleanor/matlab/bin/glider/WOD/wod05/mat/';
headerfile = 'header1cast.csv';
datafile = 'data1cast.csv';

% Clean out files, removing string '---.---'
ext4 = '.csv';
fid = fopen([input_dir,filename,ext4]);
iter=0;


fline = fgetl(fid);
while fline(1)=='#'
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    %  Read ONE CAST into header and data files
    iter = iter+1;
    fid_hdr = fopen(headerfile,'w');
    fid_data = fopen(datafile,'w');

    fline = fgetl(fid);
    while (fline(1)~=' ')&&(~strcmp(fline(1:3),'BIO'))   % First line of data
        fwrite(fid_hdr,fline);
        fprintf(fid_hdr,'\n');
        fline = fgetl(fid);
    end
    if strcmp(fline(1:3),'BIO')
        while fline(1)~='#'
            fline = fgetl(fid);
        end
        fclose(fid_hdr);
        fclose(fid_data);
    else
        while ~strcmp(fline(1:3),'END')   % line is "END OF VARIABLES ..."
            fwrite(fid_data,fline);
            fprintf(fid_data,'\n');
            fline = fgetl(fid);
        end
        fclose(fid_hdr);
        fclose(fid_data);

        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
        %  Parse the header file
        fid_hdr = fopen(headerfile);
        C = textscan(fid_hdr,'%s%s%s%s%s%s%s%s','delimiter',',','emptyValue',1);
        C1 = C{1};
        C3 = C{3};
        for n=1:length(C1)
            entry1 = cell2mat(C1(n));
            if length(entry1)>2
                entry3 = entry1(1:3);
                switch entry3
                    case {'CAS'}
                        cast_num = str2double(cell2mat(C3(n)));
                        all_casts(iter) = cast_num;
                    case {'Lat'}
                        lat = str2double(cell2mat(C3(n)));
                    case {'Lon'}
                        lon = str2double(cell2mat(C3(n)));
                    case {'Yea'}
                        yy = str2double(cell2mat(C3(n)));
                    case {'Mon'}
                        mm = str2double(cell2mat(C3(n)));
                    case {'Day'}
                        dd = str2double(cell2mat(C3(n)));
                    case {'VAR'}
                        for k=1:length(C)
                            Ck = C{k};
                            hdr(k).name = cell2mat(Ck(n));
                        end
                end
            end
        end
        fclose(fid_hdr);

        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
        %  Create data structure
        cast(iter).inst = inst;

        cast(iter).number = cast_num;
        cast(iter).lat = lat;
        cast(iter).lon = lon;
        cast(iter).yy = yy;
        cast(iter).mm = mm;
        cast(iter).dd = dd;
        cast(iter).salin = [];
        %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
        %  Parse the data file
        mydata = importdata(datafile);
        cast(iter).flag=0;
        ll = 0;
        for k=1:length(C)
            ll = ll+1;
            if length(hdr(k).name)
                hdr3 = hdr(k).name(1);

                switch hdr3
                    case 'V'
                        cast(iter).index = mydata(:,ll);
                    case 'D'
                        cast(iter).depth = mydata(:,ll);
                    case 'F'
                        cast(iter).flag = cast(iter).flag+mydata(:,ll);
                    case 'T'
                        cast(iter).temp = mydata(:,ll);
                    case 'S'
                        cast(iter).salin = mydata(:,ll);
                    case {'O','0'}
                        ll=ll-1;
                end
            end
        end
    end
    fline = fgetl(fid);
    if isempty(fline)
        break
    end
end

fclose(fid);

eval(['save ',output_dir,filename,'.mat cast']);