Code

Faster GAF sorting#4505

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jltsiren merged 14 commits intomastervgteam/vg:masterfrom faster-gaf-sortingvgteam/vg:faster-gaf-sortingCopy head branch name to clipboardJan 26, 2025

+1,794-241

Commits

Commits on Jan 22, 2025

• Building blocks for a fast GAF sorter

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• More tests for GAF sorting

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Commits on Jan 23, 2025

• Integrated GAF sorting

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• Option to use stable sorting

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• Sort directly to the final output if possible

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• Use htslib files for reading GAF

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• Error handling for GAF sorter

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Commits on Jan 24, 2025

• Use gaf_sorter in vg gamsort

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Commits on Jan 25, 2025

• zstd-compressed temporary files

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• Some tests for GAF sorting

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• Update GBWT and GBWTGraph for more efficient GBZ loading

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Commits on Jan 26, 2025

• Do not use ZSTD_defaultCLevel()

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• Don't use C++17 then

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• Some const_casts

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