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More efficient handling of long queries #18

@RagnarGrootKoerkamp

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@RagnarGrootKoerkamp

As written in future work of the paper:

Following #4, for 100bp-1kbp queries, we may want to do some of the following:

  • early abort on >k edits (Early break on distance >k #2). Maybe we can check after every 64 columns or so.
  • Make the searched region more sparse, as in Fig 3b here.
  • Do band-doubling or so for the traceback step.

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