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https://issues.apache.org/jira/browse/HBASE-1212?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=12688552#action_12688552
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Nitay Joffe commented on HBASE-1212:
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As I noted on HBASE-1274, we can try using the file names to do the sequencing:

bq. What about using something that sorts lexicographically and sorting the 
dir.listFiles we use when grabbing the store files? Then when we move around 
two files with the same sequence ids to do a merge we can rename the actual 
files.

> merge tool expects regions all have different sequence ids
> ----------------------------------------------------------
>
>                 Key: HBASE-1212
>                 URL: https://issues.apache.org/jira/browse/HBASE-1212
>             Project: Hadoop HBase
>          Issue Type: Bug
>            Reporter: stack
>
> Currently merging two regions, the merge tool will compare their sequence 
> ids.  If same, it will decrement one.  It needs to do this because on region 
> open, files are keyed by their sequenceid; if two the same, one will erase 
> the other.
> Well, with the move to the aggregating hfile format, the sequenceid is 
> written when the file is created and its no longer written into an aside file 
> but as metadata on to the end of the file.  Changing the sequenceid is no 
> longer an option.
> This issue is about figuring a solution for the rare case where two store 
> files have same sequence id AND we want to merge the two regions.

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