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Read Alignment Parallelization#98

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trevormartinj7 merged 100 commits intomasteredilytics/CRISPResso2:masterfrom trevor/alignment-parallelizationedilytics/CRISPResso2:trevor/alignment-parallelizationCopy head branch name to clipboardAug 26, 2024

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Commits

Commits on Jun 25, 2024

• Initial parallization work

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• Initial parallization work

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• Fleshed out process function, added tracking for manager dictionary

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• lots of debugging of the process function

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• parallelization achieved

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• Improved boundary function

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• Removing prints

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• removing old code

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• Failed cache generator function

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• Created single thread seq_cache generator

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• initial functioning parallelization

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• adding data to variantCache and N_ constants

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• more edits

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• replacing old aln stats

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• Fixed return values

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• changing output file

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• fixed boundary error

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• Adding more tracking of timings

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• optimized stat tracking considerably

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• removing imports and unneccesary checks

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• more logging

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• Unbalancing the processes to allow for better locking interactions

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Commits on Jun 26, 2024

• Adding amplicon name to plotting

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Commits on Jun 27, 2024

• fixing stat tracking

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• removed old code

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Commits on Jul 2, 2024

• pin numpy

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Commits on Jul 9, 2024

• Pin versions of numpy and matplotlib in CI environment (#84)

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• Merge branch 'master' of github.com:edilytics/CRISPResso2

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Commits on Jul 22, 2024

• D3-Enhancements (#78)

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• Merge branch 'master' of github.com:edilytics/CRISPResso2

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Commits on Jul 24, 2024

• old changes

  

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• removed some superfluous code

  

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• removed some superfluous code

  

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• reverting to old flow if one process

  

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• Enriched aln_stats with aligned read_length

  

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• fixed declaration bug

  

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• Fixing stats tracking for irregular reads

  

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• fixed stat tracking by multiplying variant count

  

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• adding some function explanations, cleaning up code, optimizing lock updating

  

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• Cleaned up code, potentially breaks tests

  

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• Revert "Cleaned up code, potentially breaks tests"

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• Revert "adding some function explanations, cleaning up code, optimizing lock updating"

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• replaced test branch, reverted to working version, added .upate() inside lock

  

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• checking old cython branch

  

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• reverting breaking changes

  

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• pointing back at my test branch, unreverting non breaking changes

  

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• timing log change

  

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• pin numpy

  

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• Pin versions of numpy and matplotlib in CI environment (#84)

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• pointing to correct test branch

  

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• removed debug statement

  

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• memory tracking

  

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• Replaced seq_cache with variantCache for improved memory

  

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• removing print statements

  

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• commenting out memory tracking

  

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• Removing one extra loop to improve processing time

  

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• optimizing info, removing old functions and print statements

  

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• removing empty string handling

  

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• removed empty string, reworded comments

  

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• removing uneccesary files

  

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• Merge branch 'master' into fastq-alignment-parallelization-without-cython

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Commits on Jul 25, 2024

• Merge branch 'master' into fastq-alignment-parallelization-without-cython

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• Literally minding my p's and q's

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• Reset .c files

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• Editing function comments, renaming managerCache, removing debug print statement

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Commits on Jul 29, 2024

• Initial attempt at creating a temp_variant file for memory optimization

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Commits on Jul 30, 2024

• update

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• reading and writing to tsv to save on memory

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• Merged in memory optimization branch

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• Updating pytests for equal boundary changes

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Commits on Aug 7, 2024

• Refactored write out fastq, improved tests

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Commits on Aug 8, 2024

• Replace zcat (#94)

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• Limiting plotting processes

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• Merge branch 'master' of github.com:edilytics/CRISPResso2

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Commits on Aug 9, 2024

• Fix CRISPRessoAggregate bug and other improvements (#95)

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Commits on Aug 12, 2024

• Add BAM test cases to Github Actions integration tests

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• Add "Run" to step names

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• Merge branch 'master' into cole/add-bam-tests

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Commits on Aug 13, 2024

• Point to trevor/fastq-testing test branch

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• Add in Aggregate test case to Github Actions

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• Merge branch 'master' into cole/add-bam-tests

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• parallelizing process_single_fastq_write_bam_out function

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• Merged master

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• wip parallelization for process_bam function

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Commits on Aug 14, 2024

• Fixing write out bug

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• Functional bam input parallelized function

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• Merge branch 'master' into local-fastq-alignment-parallelization-without-cython

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• cleaned up code, removed old versions of functions

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• merged cole's branch

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• trying again

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• Remove duplicate c2_tests

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• Remove commented out copy c2_tests

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Commits on Aug 16, 2024

• Updating file access to close on error, removing unnecesary bam appendings

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Commits on Aug 23, 2024

• Add percent_completeto info statements (#102)

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• Updated functions with newly merged progress percent from Cole

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Commits on Aug 26, 2024

• Minor code cleanup, removal of comments and print statements etc

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• Merge branch 'master' of github.com:edilytics/CRISPResso2

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• merging master

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• Pointing test branch back at CRISPResso2_tests master branch

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• Added checking for failed processes causing not all reads to be counted

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