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https://issues.apache.org/jira/browse/CASSANDRA-5351?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13845889#comment-13845889
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Lyuben Todorov commented on CASSANDRA-5351:
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I created a [feature branch|https://github.com/lyubent/cassandra/tree/5351] and 
rebased to trunk (old branch was too outdated) A mismatch between the number of 
tables being swapped is causing repairs to get stuck on an assert in 
DataTracker.newSSTables(...) which could explain the out-of-order key as  
LeveledManifest.lastCompactedKeys gets updated (in LeveledManifes.replace(...) 
) regardless of whether the assert passed or not.

> Avoid repairing already-repaired data by default
> ------------------------------------------------
>
>                 Key: CASSANDRA-5351
>                 URL: https://issues.apache.org/jira/browse/CASSANDRA-5351
>             Project: Cassandra
>          Issue Type: Task
>          Components: Core
>            Reporter: Jonathan Ellis
>            Assignee: Lyuben Todorov
>              Labels: repair
>             Fix For: 2.1
>
>
> Repair has always built its merkle tree from all the data in a columnfamily, 
> which is guaranteed to work but is inefficient.
> We can improve this by remembering which sstables have already been 
> successfully repaired, and only repairing sstables new since the last repair. 
>  (This automatically makes CASSANDRA-3362 much less of a problem too.)
> The tricky part is, compaction will (if not taught otherwise) mix repaired 
> data together with non-repaired.  So we should segregate unrepaired sstables 
> from the repaired ones.



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