a0b5986572f9489fe81f8339013cef773dff7ae0
wong
  Fri Jan 13 17:08:35 2012 -0800
doesn't skip empty lines now
diff --git python/lib/ucscgenomics/ucscUtils.py python/lib/ucscgenomics/ucscUtils.py
index b155e04..faa5cfb 100644
--- python/lib/ucscgenomics/ucscUtils.py
+++ python/lib/ucscgenomics/ucscUtils.py
@@ -112,25 +112,26 @@
             consensus.append(align1[i])
             consensus.append(align2[i])
 
     before = list()
     if before_i != 0:
         before.extend(list1[0:before_i])
     if before_j != 0:
         before.extend(list2[0:before_j])
     if after_i < len(list1):
         consensus.extend(list1[after_i:])
     if after_j < len(list2):
         consensus.extend(list2[after_j:])
     before.extend(consensus)
     setcon = list()
     p = re.compile('^#')
+    p2 = re.compile('^\s*$')
     for i in before:
-        if p.match(i):
+        if p.match(i) or p2.match(i):
             setcon.append(i)
             continue
         if i in setcon:
             continue
         else:
             setcon.append(i)
     
     return setcon