Lewis John McGibbney created JOSHUA-312:

             Summary: Alignment is never cached
                 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
            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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