Code

Super basic hypergeometric filter#284

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ekg merged 33 commits intomainwaveygang/wfmash:mainfrom subindex-cleanupwaveygang/wfmash:subindex-cleanupCopy head branch name to clipboardOct 21, 2024

+171-282

Commits

Commits on Oct 14, 2024

• fix: Remove debugging messages and sequence id manager state dumping

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• fix: Remove debugging messages from SequenceIdManager and computeMap

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• feat: Implement indexing and reading of multiple sub-indexes in a single file

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• fix: replace getSequenceNames() with getTargetSequenceNames()

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• feat: add debugging statements to show index and expected sequences

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• fix: Write only target subset sequences to sub-index header

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Commits on Oct 15, 2024

• feat: fix writeIndex function call in computeMap.hpp

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• refactor: Remove debugging output for sequence names in readSubIndexHeader

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• fix: remove frequent kmer tracking and checking

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• fix: Remove unused variables and functions from winSketch.hpp

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• cleanup comments about frequent kmer filter

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• remove reference to kmer frequency filter

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• feat: Add index loading for target sequence subsets

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• feat: Update Sketch constructor to load index directly from input stream

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• fix: remove duplicate declaration of indexStream

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• feat: Remove unused loadIndex method from winSketch.hpp

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• fix: Replace loadIndex with readIndex in winSketch.hpp

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• cleanup multi-index-making

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Commits on Oct 17, 2024

• feat: Replace no-hg-filter flag with hg-filter and update logic

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• fix: Revert to using --no-hg-filter while removing numerical flags

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Commits on Oct 18, 2024

• feat: Implement fixed Jaccard numerator for MashMap

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• feat: Add total reference size and estimated unique k-mers to improve Jaccard numerator calculation

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• feat: Implement information theoretic estimation of unique k-mers

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• fix: Remove duplicate declaration of fixedJaccardNumerator in map_parameters.hpp

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• fix: Add debug output for fixed Jaccard numerator

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• fix: Improve Jaccard similarity filtering logic

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• refactor: update search/replace block in computeMap.hpp

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• fix: define cutoff_j variable in computeL1CandidateRegions function

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• fix: remove debug output

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• fix: Remove debug output from computeMap.hpp

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Commits on Oct 19, 2024

• feat: Rename parameters and update CLI help

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• feat: allow hgNumerator parameter to be a double

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• fix: Replace deprecated globalJaccardNumerator with hgNumerator in computeMap.hpp

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