Prefilter mappings to save memory in batched mapping#301

Merged

ekg merged 21 commits intomainfrom prefilter

Dec 2, 2024

+125-19

Commits on Nov 25, 2024

feat: Add flag to disable sequence grouping with -G option
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feat: Implement subset filtering optimization for memory efficiency
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refactor: Improve atomic chain ID update with max subset calculation
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refactor: Improve mapping aggregation across target subsets
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check if the approx mapping flag is set to correctly detect if we are approx mapping (params are parsed later)
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refactor: Improve mapping filtering and chaining logic in parallel processing
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refactor: Move subset mapping filtering and chain ID updates to correct threads
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refactor: Modify mapping filtering to preserve merged and non-merged mappings
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feat: Add mapping filtering logic for merged and non-merged results
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fix: Update QueryMappingOutput and CombinedMappingResults to resolve compilation errors
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fix: Resolve compilation errors in computeMap.hpp mapping logic
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fix: Update computeMap.hpp to resolve compilation errors with mapping results
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fix: Refactor CombinedMappingResults to simplify mapping handling
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fix: Resolve compilation errors in computeMap.hpp by updating mapping vector handling
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refactor: Optimize chain ID generation to use sequential, smaller IDs
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refactor: Preserve chain relationships in updateChainIds by using base offset
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refactor: Implement dense chain ID mapping with compact range generation
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refactor: Move chain ID compaction to MapModule with atomic offset
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feat: Add -X flag to control self-mapping behavior with -G
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Commits on Nov 27, 2024

refactor: Remove redundant mappings parameter and use -n/--mappings for segment mapping count
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Commits on Dec 2, 2024

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