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Add dumpstrobes --seeds option for writing out the full seed vector #353

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merged 2 commits into from
Oct 2, 2023

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marcelm
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@marcelm marcelm commented Oct 2, 2023

With this, dumpstrobes --seeds genome.fa dumps the sorted randstrobes vector to standard output in a comma-separated format.

Columns:

  • hash
  • position
  • reference index
  • strobe 2 offset

I also had to move two functions in index.cpp into an anonymous namespace as otherwise the linker complains about a duplicate name (count_randstrobes exists twice).

Otherwise, we get linker errors in dumpstrobes because that also contains a
count_randstrobes function.
@ksahlin
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ksahlin commented Oct 2, 2023

Thanks! Approved.

@marcelm marcelm merged commit 1587954 into main Oct 2, 2023
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@marcelm marcelm deleted the dumpseeds branch October 2, 2023 21:12
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2 participants