--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/makewindow.py	Fri Mar 09 19:59:07 2012 -0500
@@ -0,0 +1,19 @@
+def makeWindow(filename,outfile,window):
+    window = window/2
+    f=open(filename)
+    out = open(outfile,'w')
+    for line in f:
+        flds = line.strip().split()
+        #new position
+        center = (int(flds[1]) + int(flds[2]))/2
+        start = center - window
+        end = center + window
+        if start >= 0:
+            flds[1] = str(start)
+            flds[2] = str(end)
+            out.write('\t'.join(flds)+'\n')
+    f.close()
+    out.close()
+
+import sys
+makeWindow(sys.argv[1],sys.argv[2],int(sys.argv[3]))