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1 function CFG = process_configure_rdiff(CFG)
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2 % process_configure_rDiff(CFG)
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3
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4 for i=1:length(CFG.BAM_FILES)
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5 if isempty(CFG.NAMES{i})
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6 CFG.NAMES{i}=CFG.BAM_FILES{i};
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7 end
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8 end
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9
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10 %Get the paths of the filenames
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11 for i=find(CFG.SAMPLES==1)
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12 CFG.BAM_FILES{i}=fullfile(CFG.data_dir,CFG.BAM_FILES{i});
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13 end
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14
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15 for i=find(CFG.SAMPLES==2)
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16 CFG.BAM_FILES{i}=fullfile(CFG.data_dir,CFG.BAM_FILES{i});
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17 end
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18
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19
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20 %Check that the variance functions are available if necessary
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21 if or(CFG.perform_nonparametric,CFG.perform_parametric) && length(CFG.predefined_variance_function1)<3 && isempty(CFG.variance_function_1)
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22 CFG.compute_variance_function_1=1;
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23 end
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24
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25 if or(CFG.perform_nonparametric,CFG.perform_parametric) && length(CFG.predefined_variance_function2)<3 && isempty(CFG.variance_function_2)
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26 CFG.compute_variance_function_2=1;
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27 end
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28
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29 %Check that there are sufficient samples to estimate the variance funtions
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30 if CFG.compute_variance_function_1==1
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31 if and(length(find(CFG.SAMPLES==1))<2,not(CFG.merge_sample1))
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32 error('Not sufficient samples to estimate variance function for sample 1');
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33 end
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34 end
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35
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36 if CFG.compute_variance_function_2==1
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37 if and(length(find(CFG.SAMPLES==2))<2,not(CFG.merge_sample2))
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38 error('Not sufficient samples to estimate variance function for sample 2');
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39 end
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40 end
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41
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42
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43
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44 %If a variance function can be loaded use this function and do not
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45 %compute a new one
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46 if or(CFG.perform_nonparametric,CFG.perform_parametric) && length(CFG.predefined_variance_function1)<3 && not(isempty(CFG.variance_function_1))
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47 CFG.compute_variance_function_1=0;
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48 end
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49
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50 if or(CFG.perform_nonparametric,CFG.perform_parametric) && length(CFG.predefined_variance_function2)<3 && not(isempty(CFG.variance_function_2))
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51 CFG.compute_variance_function_2=0;
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52 end
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53
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54
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55 %If a variance function can be loaded use this function and do not
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56 %compute a new one
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57 if or(CFG.perform_nonparametric,CFG.perform_parametric) && length(CFG.predefined_variance_function1)<3 && not(isempty(CFG.variance_function_1))
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58 CFG.compute_variance_function_1=0;
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59 end
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60
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61 if or(CFG.perform_nonparametric,CFG.perform_parametric) && length(CFG.predefined_variance_function2)<3 && not(isempty(CFG.variance_function_2))
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62 CFG.compute_variance_function_2=0;
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63 end
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64
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65
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66
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