Github user afs commented on the issue:

    https://github.com/apache/jena/pull/212
  
    Revision to `deleteFrom`:  loop on src if (srcSize < 1000 || dstSize > 
2*srcSize)
    
    That is, when dst is small, do the loop/contains thing. 
    
    This is more conservative and so less disturbing existing code but catches, 
I hope, the case of small destination (target) graph, typically in-memory, and 
large src graph (some large database).
    
    1000 is a guess - 10,000 is better maybe?


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