Code

Addition of multithreading#419

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nickjcroucher merged 87 commits intomasternickjcroucher/gubbins:masterfrom v3_devnickjcroucher/gubbins:v3_devCopy head branch name to clipboardNov 15, 2024

+1,265-560

Commits

Commits on Apr 17, 2024

• Optimise recombination identification

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  fbb5df9

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• Merge pull request #404 from nickjcroucher/master

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Commits on Apr 18, 2024

• Fix comment typo

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• Restore master version to check CI

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• Restore filtering block functions

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• Update get_blocks function

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• Update downstream recombinations function

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• Revert "Update get_blocks function"

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• Add tree iteration functions

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• Access lists of nodes at different depths

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• Revert breaking changes

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• Prototype multithreading function

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• Remove node counter

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Commits on Apr 19, 2024

• Rename variables to help rewrite

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• Introduce new data structures

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• Switch recursion to loop

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• Correct indentation of sequence storage

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• Add pthreads to compilation commands

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• Correct length of sequence stored

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• Correct array parsing

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• Fix conditional test

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• Fix NULL initialisation

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Commits on Apr 20, 2024

• Fix memory clearing error

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• Fix memory allocation statements

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• Update ordering of file with new function implementation

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Commits on Apr 21, 2024

• Changes to formatting

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Commits on Apr 22, 2024

• Multithread branch sequence reconstruction

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• Remove potential memory leaks

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  a41030f

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• Update memory management

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• Simplify code structure

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• Test one thread

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Commits on Apr 23, 2024

• Fix memory management

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  65cce5b

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• Parallelise gap inference

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• Remove obsolete function

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• Modularise functions

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• Fix iterator

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• Fix counter value

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• Remove extra iterator

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• Minor change to ll value

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• Remove obsolete sequence retrieval

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• Enable thread safe printing

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• Enable spectification of thread number

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• Enable multithreaded recombination detection

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• Bump version

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• Update gubbins arguments

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• Update gubbins arguments

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• Update gubbins arguments

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• Fix missing positional argument

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• Reorder gubbins flags

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• Rename threaded functions

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• Convert gap function to loop from recursive

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Commits on Apr 24, 2024

• Data structures for looping

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• Fix function definitions

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• Fix genome length calculations

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• Fix SNP statistic calculation

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• Correct function name

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• Update expected tree following recombination length recalculation

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• Update after adjusting recombination length calculation

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• Add stats test

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• Parallelise gap function

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• Set values by index not name

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• Avoid copying nodes when parallelising

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Commits on May 27, 2024

• Update IQTREE multithreading argument

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• Add ska.rust citation

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Commits on May 28, 2024

• Change CI for new OSX version

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• Change CI again for new OSX version

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• Remove chown command

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• Add miniconda installation

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• Change miniconda installation

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• Change CI file indentation

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• Downgrade macos until dependencies upgraded

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Commits on May 29, 2024

• Change line width based on number of samples

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Commits on May 31, 2024

• Add script for extracting recombinant sequences

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• Add extract_recombinant_sequences.py

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• Make script executable

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Commits on Jun 3, 2024

• Add test_extract_recombination_sequences

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• Add documentation for extract_recombinant_sequences.py

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Commits on Jun 7, 2024

• Improve AVX RAxML selection

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Commits on Jun 17, 2024

• Fix calculation of recombination lengths

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• Enable recombination length calculation with gaps

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• Calculate recombination length including gaps

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• Add argument to calculate_number_of_bases_in_recombinations_excluding_gaps

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• Update function name

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• Test if rec length tests cause failure

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• Test if rec length tests cause failure

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  b0ddb28

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• Update expected stats file

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• Restore rec length tests

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