--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/process_configure_rdiff.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,66 @@
+function CFG = process_configure_rdiff(CFG)
+  %  process_configure_rDiff(CFG)
+
+for i=1:length(CFG.BAM_FILES)
+    if isempty(CFG.NAMES{i})
+        CFG.NAMES{i}=CFG.BAM_FILES{i};
+    end
+end
+
+%Get the paths of the filenames
+for i=find(CFG.SAMPLES==1)
+  CFG.BAM_FILES{i}=fullfile(CFG.data_dir,CFG.BAM_FILES{i}); 
+end
+
+for i=find(CFG.SAMPLES==2)
+  CFG.BAM_FILES{i}=fullfile(CFG.data_dir,CFG.BAM_FILES{i}); 
+end
+
+
+%Check that the variance functions are available if necessary
+if or(CFG.perform_nonparametric,CFG.perform_parametric) &&  length(CFG.predefined_variance_function1)<3 && isempty(CFG.variance_function_1)
+    CFG.compute_variance_function_1=1;
+end
+    
+if or(CFG.perform_nonparametric,CFG.perform_parametric) &&  length(CFG.predefined_variance_function2)<3 && isempty(CFG.variance_function_2)
+    CFG.compute_variance_function_2=1;
+end
+
+%Check that there are sufficient samples to estimate the variance funtions
+if CFG.compute_variance_function_1==1
+  if and(length(find(CFG.SAMPLES==1))<2,not(CFG.merge_sample1))
+        error('Not sufficient samples to estimate variance function for sample 1');
+    end
+end
+
+if CFG.compute_variance_function_2==1
+      if and(length(find(CFG.SAMPLES==2))<2,not(CFG.merge_sample2))
+        error('Not sufficient samples to estimate variance function for sample 2');
+    end
+end
+
+
+
+%If a variance function can be loaded use this function and do not
+%compute a new one
+if or(CFG.perform_nonparametric,CFG.perform_parametric) &&  length(CFG.predefined_variance_function1)<3 && not(isempty(CFG.variance_function_1))
+    CFG.compute_variance_function_1=0;
+end
+    
+if or(CFG.perform_nonparametric,CFG.perform_parametric) &&  length(CFG.predefined_variance_function2)<3 && not(isempty(CFG.variance_function_2))
+    CFG.compute_variance_function_2=0;
+end
+
+   
+%If a variance function can be loaded use this function and do not
+%compute a new one
+if or(CFG.perform_nonparametric,CFG.perform_parametric) &&  length(CFG.predefined_variance_function1)<3 && not(isempty(CFG.variance_function_1))
+    CFG.compute_variance_function_1=0;
+end
+    
+if or(CFG.perform_nonparametric,CFG.perform_parametric) &&  length(CFG.predefined_variance_function2)<3 && not(isempty(CFG.variance_function_2))
+    CFG.compute_variance_function_2=0;
+end
+    
+
+