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Alignment with ksw2 and WFA2-lib#242

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marcelm wants to merge 23 commits intomainksahlin/strobealign:mainfrom wfaksahlin/strobealign:wfaCopy head branch name to clipboard

+1,385-1,067

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Commits on Feb 24, 2023

• Move Aligner into a separate file

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• Remove some unused code

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• Rename ref_offset to ref_start

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• Add query_start and query_end attributes to aln_info

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• Remove hamming_align soft_left/soft_right parameters

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• Remove aln_info.global_ed

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• Move SSW files to an ssw/ subdirectory

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• Add aln_info.ref_end

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• Rename aln_info.ed to edit_distance

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• Consistently use query, ref as parameter order

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• Make WFA2-lib available to the build

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• Temporary static linking fix

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• Update ksw2 to the most recent upstream version

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• Move ksw2 files to a subdirectory and add license

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• Add a Cigar class

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• Start using WFA2 (for global alignment of the NAM)

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• Start ksw2 wrapper

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• Implement right extension with ksw2

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• Implement left extension with ksw2

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• Implement Cigar::edit_distance() to count edits correctly in ksw_extend

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• ksw’s built-in CIGAR-reversing capability does not seem to work

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• Re-add the hamming_align optimization

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• Let aln_info.cigar be a Cigar object

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