development release: conversion of ReadDataset to use BAM files

[erange.git] / MakeRdsFromBam.py

diff --git a/MakeRdsFromBam.py b/MakeRdsFromBam.py
index 13c901332b2c54dcf6b4033a6633ec0e074da782..b16bccd2da0fae8b7e6ed85c20237286e9623823 100644 (file)
--- 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: