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Add syncmers at ends of reads #452

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Add syncmers at ends of reads #452

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Commits on Oct 7, 2024

  1. Add syncmers at the ends of reads as seeds without auxiliary hash 

    Increases the number of seeds per read by 2*w_min seeds
    @ksahlin @marcelm
    ksahlin authored and marcelm committed Oct 7, 2024
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  2. Make RandstrobeIterator/-Generator yield the same results

    @marcelm
    marcelm committed Oct 7, 2024
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  3. Ensure unmappable.41 really is unmappable 

    Randstrobes that have no downstream partner at least w_min syncmers away get
their second hash set to 0, which means in the case of multi-context seeds
that the primary/main hash is also zero (because it is the smaller of the
two).

When this is done both for the reference and for queries, we get spurious
hits for all randstrobes towards the ends of queries (they get mapped to the
end of the reference).

Using the hash of the primary syncmer also as hash for the second syncmer
gets rid of the problem.
    @marcelm
    marcelm committed Oct 7, 2024
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  4. Simplify: Iterating zero times gives same result

    @marcelm
    marcelm committed Oct 7, 2024
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