--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/tests/get_nonparametric_masks.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,24 @@
+function [MASKS]=get_nonparametric_masks(CFG,reads1,reads2)
+
+%What fracitons should be choosen for the cutoff
+cen_arr=0.1:0.1:1;
+
+% Define the mask which should be used in order to mask high
+% expresse genes
+MASKS=zeros(length(cen_arr),size(reads1,2));
+
+COUNTER=1;
+for censor_frac= cen_arr  
+    temp_reads1=reads1;
+    temp_reads2=reads2;
+    %cut to relvant position
+    read_coverage=sum(reads1,1)+sum(reads2,1); 
+    % get positions with a positive coverage
+    nonzero_position=read_coverage>0;
+    %Determine the cutoff values
+    sorted_coverage=sort(read_coverage(nonzero_position));
+    nr_of_nonzero_positions=sum(nonzero_position);
+    relevant_positions=read_coverage<=sorted_coverage(ceil(nr_of_nonzero_positions*censor_frac));
+    MASKS(COUNTER,relevant_positions)=1;
+    COUNTER=COUNTER+1;
+end