Fix: Do not report failed alignments

ksahlin / strobealign

Aligns short reads using dynamic seed size with strobemers

MIT License

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Closed marcelm closed 1 month ago

marcelm commented 1 month ago

Refactor Aligner::align to return an std::optional<Alignment>. This way, we don’t have to rely on special vales for the attributes of an alignment to represent failed alignments.
Fix the problem that we did not detect failed calls to ssw_align

Marked as draft because extend_seed and rescue_align don’t quite work, yet, with this change.

Closes #424

ksahlin commented 1 month ago

approved

marcelm commented 1 month ago

Fixed the tests. Also, added a commit that clarifies what -U does both in the command-line help text and the README.