--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/tools/read_utils/clip_reads.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,19 @@
+function [reads1]=clip_reads(reads1,CLIP_NUCL)
+% This function clips the first CLIP_NUCL bases from reads1
+if or(size(reads1,1)==0,size(reads1,2)==0)
+  return
+end
+
+for C_ITER=1:CLIP_NUCL
+  %Clip the first bases
+  [TEMP,FIRST_VECT]=max(reads1,[],2);
+  FIRST_MASK=sparse((1:length(FIRST_VECT))',FIRST_VECT,ones(length(FIRST_VECT),1),size(reads1,1),size(reads1,2));
+  reads1(FIRST_MASK>0)=0;
+  
+  %Clip the last bases 
+  [TEMP,FIRST_VECT]=max(reads1(:,end:(-1):1),[],2);
+  FIRST_VECT=size(reads1,2)-FIRST_VECT+1;
+  FIRST_MASK=sparse((1:length(FIRST_VECT))',FIRST_VECT,ones(length(FIRST_VECT),1),size(reads1,1),size(reads1,2));
+  reads1(FIRST_MASK>0)=0;
+  
+end