X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=erange.git;a=blobdiff_plain;f=MakeRdsFromBam.py;fp=MakeRdsFromBam.py;h=b16bccd2da0fae8b7e6ed85c20237286e9623823;hp=13c901332b2c54dcf6b4033a6633ec0e074da782;hb=cfc5602b26323ad2365295145e3f6c622d912eb4;hpb=c4561c55cfa9726530c6777b6515c4ef66306b2f

diff --git a/MakeRdsFromBam.py b/MakeRdsFromBam.py
index 13c9013..b16bccd 100644
--- a/MakeRdsFromBam.py
+++ b/MakeRdsFromBam.py
@@ -418,13 +418,13 @@ def getMismatches(mismatchTag, querySequence="", sense="+", logErrors=False):
 
 
 def getSpliceBounds(start, readsize, cigarTupleList):
-    stopR = int(start + readsize)
     offset = 0
 
     for operation,length in cigarTupleList:
         if operation == 3:
             stopL = int(start + offset)
             startR = int(stopL + length)
+            stopR = int(startR + readsize - offset)
 
             return start, startR, stopL, stopR
         else: