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https://issues.apache.org/jira/browse/JOSHUA-312?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15586063#comment-15586063
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Matt Post commented on JOSHUA-312:
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This is fixed with commit 301f301cdcad5ab49c8465506791e5f117e1c944 (just
pushed). The problem was that I changed the structure of the alignment splits,
and did not update the paths for Berkeley aligner. Sorry about the trouble!
> Even though alignment is cached, it is always re-done in pipeline re-execution
> ------------------------------------------------------------------------------
>
> Key: JOSHUA-312
> URL: https://issues.apache.org/jira/browse/JOSHUA-312
> Project: Joshua
> Issue Type: Improvement
> Components: alignment
> Affects Versions: 6.0.5
> Reporter: Lewis John McGibbney
> Assignee: Lewis John McGibbney
> Priority: Critical
> Fix For: 6.2
>
>
> Say if a pipeline fails after alignment. The alignment result is never cached
> and it becomes necessary to undertake alignment... again!
> We should investigate the process for caching alignments as it would really
> speed up rerunning end-to-end pipelines for large input datasets.
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