Remove duplicate alphabets and replace seqan2::String#109

Draft

eaasna wants to merge 43 commits into

mainfrom

Commits on Jun 26, 2024

Commits on Jul 11, 2024

Commits on Jul 12, 2024

Read query sequences of adaptor alphabet in addition to native seqan alphabets
eaasna
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Commits on Jul 31, 2024

Split and prefilter adapted sequences without stellar search
eaasna
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Commits on Aug 2, 2024

Commits on Aug 4, 2024

Adapted database sequence input
eaasna
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Commits on Aug 5, 2024

Commits on Aug 6, 2024

Commits on Aug 7, 2024

Fix segment range and add kmer shape to index
eaasna
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Commits on Aug 8, 2024

Commits on Aug 12, 2024

Refactor database ID mapping and segments
eaasna
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Commits on Aug 13, 2024

Try to make stellar finder
eaasna
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Commits on Aug 15, 2024

Commits on Aug 16, 2024

Try to verify seqan2 segments of adapted alphabet type
eaasna
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Commits on Aug 20, 2024

Commits on Aug 21, 2024

Try to pass query segment parameters in shopping carts
eaasna
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Commits on Aug 22, 2024

Commits on Aug 23, 2024

Fixup: still cannot equality compare std::span
eaasna
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Commits on Aug 30, 2024

Replace seqan2::StringSet and String with std::vector in bestExtension
eaasna
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Commits on Sep 2, 2024

Fixup
eaasna
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Commits on Sep 3, 2024

Remove faulty global alignment
eaasna
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Commits on Sep 6, 2024

Pass reference to std::span to make sure that object survives
eaasna
committed

Commits on Sep 9, 2024