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Refactor low-level parsing and hashing #29

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@camillescott camillescott commented Apr 1, 2022

  • Add a kmer iterator compliant with STL InputIterator
  • Add a kmer iterator that skips invalid positions
  • Add a parser that does not validate on initial sequence read
  • Maybe: once-again remove exceptions from low level validation, in favor of std::variant with error codes.
  • Clean up and centralize exception handling
  • Remove all raw C-strings from hashshifter and extenders

For the latter: exceptions in the validation and hashing code introduces approximately 20% overhead! I removed them at one point, but added them back in because of some edge cases.

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