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https://issues.apache.org/jira/browse/LUCENE-2680?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=12928078#action_12928078
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Jason Rutherglen commented on LUCENE-2680:
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This brings up another issue which is we're blindly iterating over docs in a 
segment reader to delete, even if we can know ahead of time that the reader's 
docs are going to exceed the term/query's docid-upto (from the max doc of the 
reader).  In applyDeletes we're opening a term docs iterator, though I think 
we're breaking at the first doc and moving on if the docid-upto is exceeded.  
This term docs iterator opening can be skipped.

> Improve how IndexWriter flushes deletes against existing segments
> -----------------------------------------------------------------
>
>                 Key: LUCENE-2680
>                 URL: https://issues.apache.org/jira/browse/LUCENE-2680
>             Project: Lucene - Java
>          Issue Type: Improvement
>            Reporter: Michael McCandless
>             Fix For: 4.0
>
>         Attachments: LUCENE-2680.patch, LUCENE-2680.patch, LUCENE-2680.patch
>
>
> IndexWriter buffers up all deletes (by Term and Query) and only
> applies them if 1) commit or NRT getReader() is called, or 2) a merge
> is about to kickoff.
> We do this because, for a large index, it's very costly to open a
> SegmentReader for every segment in the index.  So we defer as long as
> we can.  We do it just before merge so that the merge can eliminate
> the deleted docs.
> But, most merges are small, yet in a big index we apply deletes to all
> of the segments, which is really very wasteful.
> Instead, we should only apply the buffered deletes to the segments
> that are about to be merged, and keep the buffer around for the
> remaining segments.
> I think it's not so hard to do; we'd have to have generations of
> pending deletions, because the newly merged segment doesn't need the
> same buffered deletions applied again.  So every time a merge kicks
> off, we pinch off the current set of buffered deletions, open a new
> set (the next generation), and record which segment was created as of
> which generation.
> This should be a very sizable gain for large indices that mix
> deletes, though, less so in flex since opening the terms index is much
> faster.

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