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Prefilter mappings to save memory in batched mapping #301

Merged
merged 21 commits into from
Dec 2, 2024
Merged

Prefilter mappings to save memory in batched mapping #301

merged 21 commits into from
Dec 2, 2024

Commits on Nov 25, 2024

  1. feat: Add flag to disable sequence grouping with -G option

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    ekg committed Nov 25, 2024
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  2. feat: Implement subset filtering optimization for memory efficiency

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    ekg committed Nov 25, 2024
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  3. refactor: Improve atomic chain ID update with max subset calculation

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  4. refactor: Improve mapping aggregation across target subsets

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  5. check if the approx mapping flag is set to correctly detect if we are… 

    … approx mapping (params are parsed later)
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  6. refactor: Improve mapping filtering and chaining logic in parallel pr… 

    …ocessing
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  7. refactor: Move subset mapping filtering and chain ID updates to corre… 

    …ct threads
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  8. refactor: Modify mapping filtering to preserve merged and non-merged … 

    …mappings
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    ekg committed Nov 25, 2024
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  9. feat: Add mapping filtering logic for merged and non-merged results

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    ekg committed Nov 25, 2024
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  10. fix: Update QueryMappingOutput and CombinedMappingResults to resolve … 

    …compilation errors
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    ekg committed Nov 25, 2024
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  11. fix: Resolve compilation errors in computeMap.hpp mapping logic

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    ekg committed Nov 25, 2024
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  12. fix: Update computeMap.hpp to resolve compilation errors with mapping… 

    … results
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  13. fix: Refactor CombinedMappingResults to simplify mapping handling

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  14. fix: Resolve compilation errors in computeMap.hpp by updating mapping… 

    … vector handling
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    ekg committed Nov 25, 2024
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  15. refactor: Optimize chain ID generation to use sequential, smaller IDs

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    ekg committed Nov 25, 2024
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  16. refactor: Preserve chain relationships in updateChainIds by using bas… 

    …e offset
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  17. refactor: Implement dense chain ID mapping with compact range generation

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    ekg committed Nov 25, 2024
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  18. refactor: Move chain ID compaction to MapModule with atomic offset

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    ekg committed Nov 25, 2024
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  19. feat: Add -X flag to control self-mapping behavior with -G

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    ekg committed Nov 25, 2024
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Commits on Nov 27, 2024

  1. refactor: Remove redundant mappings parameter and use -n/--mappings f… 

    …or segment mapping count
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    ekg committed Nov 27, 2024
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Commits on Dec 2, 2024

  1. Merge branch 'main' of github.com:waveygang/wfmash into prefilter

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    ekg committed Dec 2, 2024
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