Code

Smooth chain#272

Code

Merged

ekg merged 29 commits intomainwaveygang/wfmash:mainfrom smooth-chainwaveygang/wfmash:smooth-chainCopy head branch name to clipboardSep 20, 2024

+352-287

Commits

Commits on Sep 12, 2024

• make the direction hard cutoff in chaining more correct

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  committed
  9740f8f

• more stringent query based sort

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  committed
  41e84af

Commits on Sep 14, 2024

• feat: Implement new chaining logic for mapping merging

  ekg

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  d7ca6aa

• feat: Apply chaining logic to second mapping and sort chain pairs in ascending order

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  09242d8

• feat: Modify mergeMappingsInRange function to improve merging logic

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  869da99

• simplify sorting and just keep best chain pair option around

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  68c9df1

• get rid of axis weighted distance

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  0e8bcc9

• comment cleanup

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  fefb4ee

• refactor: processChainWithSplits

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  377f0c5

• cleanup decision to chain

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  810ce0a

• best-buddy chain merging

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  cb94726

Commits on Sep 15, 2024

• feat: Implement filtering based on maximally merged chains

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  d33a392

• feat: Restructure mapping and filtering logic

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  6401eba

• feat: add filterNonMergedMappings function

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  29ceaa2

• one codepath for mapping chain processing

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  90fe5b6

• remove unused block coordinate info

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  c7c171e

• simplify maximally merged filter

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  972222d

• fix: Modify FASTA file mapping to allow self-mapping

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  99b6681

• feat: Implement improved mapping merging and filtering

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  0222496

Commits on Sep 16, 2024

• fix: Update distance calculation in range merging to account for strand direction

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  c4408b7

• refactor: Improve distance calculation logic in computeMap.hpp

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  5fb526e

• refactor: Ensure all fields in merged mappings are properly initialized

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  c3e2b02

Commits on Sep 17, 2024

• feat: Instrument the Lee plane sweep filter algorithm

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  c89f1b0

• feat: Add detailed mapping information to debug statements

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  c67c73b

• fix: Recalculate blockNucIdentity and handle edge cases in score calculation

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  7c14341

• fix: Remove debug statements from liFilterAlgorithm

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  60ba144

• fix: Remove debug statements from markGood function

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  9bdef53

Commits on Sep 18, 2024

• fix: Correct calculation of query_end and target_end in tail patching

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  cd0542e

• add pafcheck to validation

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  240a0d3